Tag: BBMap

Batch and Sample correction for downstream analysis using DESeq2

Hello everyone, I am an absolute beginner on sequencing analysis and DESeq2, so please forgive me for possibly mundane questions. I have tried to look up different methods, but couldn’t find a fitting answer yet. I am currently working with sequencing data derived from an Illumina sequencer. The data is…

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Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir

Participants and blood collection A total of n = 23 HIV-1 seropositive individuals on stably suppressive ART were included in this study (Supplementary Table 1). Participants were recruited at Ghent University Hospital. 2/23 individuals are female, 21/23 are male; the limited representation of female individuals in our study is a direct reflection of…

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TWAS revealed significant causal loci for milk production and its composition in Murrah buffaloes

Cao, C. et al. Power analysis of transcriptome-wide association study: Implications for practical protocol choice. PLoS Genet. 17(2), e1009405 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  De Camargo, G. M. F. et al. Prospecting major genes in dairy buffaloes. BMC Genomics 16, 1–14 (2015). Article  Google Scholar  El-Halawany, N….

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Merge overlapping paired end reads from BAM file.

Merge overlapping paired end reads from BAM file. 0 Hi everyone, Using Trimmomatic and then HISAT2, I have aligned 300 RNA fastq samples (NovaSeq6000, RNA sequencing, paired-end, 150bp sequencing). I have found a percentage of overlapping paired end reads (read through) in the 300 .bam files. I found the overlaps…

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Thyroid hormone-regulated chromatin landscape and transcriptional sensitivity of the pituitary gland

Mouse genetic models The ThrbHAB allele expresses TRβ proteins (TRβ1 and TRβ2) fused to a peptide with a hemagglutinin (HAx2) tag and a site for biotinylation by prokaryotic BirA ligase, modified from a published tag30. The tag was inserted at the endogenous Thrb gene by homologous recombination in W9.5 (129/Sv)…

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MetaSPAdes genome assembly (shotgun metagenome singleend) – usegalaxy.org support

Busrak December 11, 2023, 3:31pm 1 Hi friends, Metagenomic single end raw data with cut adapt‘Maximum error rate 0.3’Match times: 1Minimum overlap length:3minimum lenght: 15Max N: 0.3Max expected errors: 30 parameters.Then I aligned the host genome with gallus gallus with BBmap tool. I want to Assembly unmapped read. However, MetaSPAdes…

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Java class error message when using BBDuk

Java class error message when using BBDuk 0 I am trying to run BBDuk to quality trim and filter my illumina whole genome sequences. I have used other trimming scripts before and have not had a problem. Although this is my first time preprocessing sequencing data from Quantseq samples. I…

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Debian — Details of source package bbmap in bookworm

Links for bbmap Debian Resources: Maintainers: External Resources: The following binary packages are built from this source package: bbmap BBTools genomic aligner and other tools for short sequences bbmap-jni short read aligner and other bioinformatic tools – JNI library Other Packages Related to bbmap adep: debhelper-compat (= 13) Package not…

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Yes .. BBMap can do that!

NOTE: This collection was originally posted at SeqAnswers.com. Creating a copy here to preserve the information.Part I is available here: Yes .. BBMap can do that! – Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)Part II is available here: Yes .. BBMap can…

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Alfalfa vein mottling virus, a novel potyvirid infecting Medicago sativa L. | Virology Journal

Plant material Five alfalfa plants (stems and leaves) were sampled from each of the four different fields, 10–15 acres in size, located in Yuma Country, Arizona, USA. Geographic coordinates of the alfalfa fields and the adjacent crops are shown in Table 1. Table 1 Geographic locations of alfalfa fields Total…

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Quast Genome assembly Quality (Galaxy Version 5.2.0+galaxy1) – usegalaxy.org support

Busrak November 29, 2023, 9:55am 1 Hi dear galaxy family, When I put my metagenome single read Megahit assembly data into Quast, I encounter the following error code. How can I solve this problem? Assembly_with_MEGAHIT_on_data_658 /usr/local/opt/quast-5.2.0/metaquast.py –single /jetstream2/scratch/main/jobs/53997042/inputs/dataset_f68c8b4a-bea0-4985-8324-4c64cdbe4d6d.dat –labels Assembly_with_MEGAHIT_on_data_658 -o outputdir –max-ref-num 50 –m 822: Quast on data 196…

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Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cell Ranger.

Looks like 10x has example datasets on their web site. Will take a look to see what these BC sequences look in reality. Should be possible to bin them using seal.sh from BBMap. Edit: From one of the test datasets it is possible to see these BC barcodes in Read…

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BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity

Hello, I know Brian is sometimes around, but here is my command: while read p; do callvariants.sh in=${p}.recal.bam ploidy=2 vcf=${p}.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g ; done <ID java -ea -Xmx50g -Xms50g -cp /home/alessandro/software/bbmap/current/ var2.CallVariants in=ancestor.recal.bam ploidy=2 vcf=ancestor.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g Executing var2.CallVariants [in=ancestor.recal.bam, ploidy=2, vcf=ancestor.20score.vcf, useiden tity=f, overwrite=true, ref=Adineta_vaga.fsa,…

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filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts

filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts 0 hi folks, apologies if this has been answered elsewhere. I’m using read mapping to quantitate the abundance of viral metagenome assembled genomes (MAGs) across samples and I’d like to do a bit of data cleaning that’s…

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Accepted bbmap 39.06+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 24 Nov 2023 11:55:22 +0100 Source: bbmap Architecture: source Version: 39.06+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Changes: bbmap (39.06+dfsg-1) unstable; urgency=medium . * New upstream version 39.06+dfsg * java_syntax.patch: delete: applied…

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Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost

Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article  Google Scholar  Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…

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BBMap : NH:i:1 and XT:A:R

BBMap : NH:i:1 and XT:A:R 0 Hi, I aligned some paired-end reads on hg19 and found some strange stuff (at least for me..). Some reads have NH:i:1 i.e. the read aligned in one position and XT:A:R i.e. XT:A:R flag indicates that the second read is repetitive. I don’t understand how…

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Do threads matter for host DNA removal with bbmap?

Do threads matter for host DNA removal with bbmap? 1 Hello, I want to use bbmap to filter out host sequences from my metagenomics reads. It is my understanding that bbmap calculates the insert size independently for each thread that it is run on, and I am trying to figure…

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How do I know how much memory to use when piping to with BBMap suite (OutOfMemoryError)?

How do I know how much memory to use when piping to with BBMap suite (OutOfMemoryError)? 1 pv trimmomatic.fastq.gz | reformat.sh int=f in=stdin.fastq.gz out=stdout.fasta | dedupe.sh in=stdin.fasta out=trimmomatic.dedupe.fasta | clumpify.sh in=stdin.fasta out=trimmomatic.dedupe.clumpify.fasta.gz My gzipped file size is 40G. I specified 250G on our server but still got the issue. I…

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Can clumpify.sh be used in a streaming fashion downstream of bcl-convert

Can clumpify.sh be used in a streaming fashion downstream of bcl-convert 0 Hi I wanted to know if it is possible to use clumpify.sh in a streaming fashion – like one would do with bwa mem …. | samtools I would like to demultiplex with bcl-convert and on the fly,…

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Index of /ubuntu/pool/universe/b/bbmap

Name Last modified Size Description Parent Directory   –   bbmap-jni_38.79+dfsg-1_amd64.deb 2020-02-27 14:23 23K   bbmap-jni_38.90+dfsg-1_amd64.deb 2021-02-05 14:24 23K   bbmap-jni_38.94+dfsg-2_amd64.deb 2021-10-19 08:55 25K   bbmap_38.79+dfsg-1.debian.tar.xz 2020-02-27 14:13 22K   bbmap_38.79+dfsg-1.dsc 2020-02-27 14:13 2.0K   bbmap_38.79+dfsg-1_all.deb 2020-02-27 14:23 5.0M   bbmap_38.79+dfsg.orig.tar.xz 2020-02-27 14:13 4.1M   bbmap_38.90+dfsg-1.debian.tar.xz 2021-02-05 14:24 22K  …

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Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms

Bond, R. & Loeffler, A. What’s happened to Staphylococcus intermedius? Taxonomic revision and emergence of multi-drug resistance. J. Small Anim. Pr. 53, 147–154 (2012). Article  CAS  Google Scholar  Carroll, K. C., Burnham, C. D. & Westblade, L. F. From canines to humans: clinical importance of Staphylococcus pseudintermedius. PLoS Pathog. 17,…

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Invasive Californian death caps develop mushrooms unisexually and bisexually

Mushroom collecting Sporocarps were collected from various herbaria and during three expeditions to Point Reyes National Seashore (PRNS), California in 2004, 2014 and 2015, and in 2015 from three sites in Portugal. A total of 86 sporocarps were collected: 67 Californian sporocarps (one early herbarium sample dates to 1993), 11…

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The Fundamentals of Metagenomics | Devpost

Inspiration Computational Biology allows for the intersection of biology and computing for technological innovations and optimizations in genomics, modeling systems, biology, phylogenetics, etc. In our project, we chose to focus on studying the structure and function of sequences from a community of organisms, like on human skin, in the soil,…

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Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes | BMC Microbiology

Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13:260–70. Article  CAS  PubMed  PubMed Central  Google Scholar  Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat Med. 2018;24:392 NIH Public Access. Article …

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Accepted bbmap 39.03+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 19 Oct 2023 22:23:06 +0200 Source: bbmap Architecture: source Version: 39.03+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Pierre Gruet <p…@debian.org> Changes: bbmap (39.03+dfsg-1) unstable; urgency=medium . * Team upload * Fixing some syntax issues linked…

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Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales

Quesada A, Vincent WF. Strategies of adaptation by antarctic cyanobacteria to ultraviolet radiation. Eur J Phycol. 1997;32:335–42. Article  Google Scholar  Genuário DB, Corrêa DM, Komárek J, Fiore MF. Characterization of freshwater benthic biofilm-forming Hydrocoryne (Cyanobacteria) isolates from Antarctica. J Phycol. 2013;49:1142–53. Article  PubMed  Google Scholar  Makhalanyane TP, Valverde A, Gunnigle…

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Aligner with statistics included?

Aligner with statistics included? 1 Hello, Is there a long range aligner that could make a statistics outlook listing how many SNP, indels etc are observed in the alignment itself? Thank you aligner alignment • 203 views BBTools’ callvariants.sh calls variants only from the alignments. So: callvariants.sh in=nxyxx.bam ref=ref.fa yields:…

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checkstrand tool (from BBMap suite) question

checkstrand tool (from BBMap suite) question 0 Brian Bushnell : I was looking at checkstrand.sh application included in the latest version of BBMap. While running a test analysis using a human sample I noticed that the output for the tool was identical in following two scenarios using a single end…

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Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle

Falkowski P. G., Raven J. A. Aquatic Photosynthesis (Princeton Univ. Press, 2013). Sanchez-Baracaldo, P., Bianchini, G., Wilson, J. D. & Knoll, A. H. Cyanobacteria and biogeochemical cycles through earth history. Trends Microbiol. 30, 143–157 (2022). Article  CAS  PubMed  Google Scholar  Blankenship, R. E. Early evolution of photosynthesis. Plant Physiol. 154,…

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How to trim bases with bbduk.sh

How to trim bases with bbduk.sh 1 Hi, I am using BBMAP following command to trim adapter sequences from the fastq files. bbduk.sh -Xmx1g \ in1=1_R1_001.fastq.gz \ in2=1_R2_001.fastq.gz \ out1=1_R1_001-trimmed.fastq.gz \ out2=1_R2_001-trimmed.fastq.gz \ literal=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \ qtrim=rl \ trimq=20 \ ktrim=r \ k=16 \ filterpolyg=5 \ tbo tpe Can anyone let…

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MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data

Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…

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Average Coverage after Assembly (Spades)

Average Coverage after Assembly (Spades) 1 Hi, I would like to know to average coverage of my assemblies (gotten by spades). I ran bbmap to mapping my reads (the same ones I used to make the assembly) to the assembly. But I am not really sure that is the way…

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Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning [PeerJ]

Introduction The rapid proliferation of high-throughput sequencing in metagenomics, combined with the advancement of scalable computational tools, has allowed scientists to digitally isolate tens of thousands of microbial genomes from large collections of metagenomic datasets (Nayfach et al., 2021). Although these genomes are only the tip of the iceberg of…

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A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Field sample collection Topsoil samples (0–15 cm, roughly 0.5 m3) from replicate field plots were collected from the Hopland Research and Extension Center (HREC) in Northern California, which is unceded land of the Shóqowa and Hopland People, on August 28th, 2018 after experiencing mean annual precipitation during the rainy season, see our…

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Quantify the number of sequences in common paired-end sequencing data

Quantify the number of sequences in common paired-end sequencing data 1 Hello, I have two fastq files with the forward(Read1) and reverse(Read2) paired reads. How could I count the number of sequences in common between Read1.fastq and Read2.fastq files? (I mean, since they have the same SeqID) And, how could…

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Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety

Study design We set up a prospective, double-blinded, randomised, placebo-controlled intervention study that was performed in our academic hospital, the Amsterdam University Medical Centres location AMC in the Netherlands. After passing screening, 24 subjects with MetSyn were randomised to receive a sterile FFT from a lean healthy donor or a…

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Demultiplexing based on dual indices in headers while allowing 1 mismatch to each index

Demultiplexing based on dual indices in headers while allowing 1 mismatch to each index 1 Hey all, I am looking for a tool that will help me demultiplexe my Novaseq samples by two dual indices in the headers. Since I have designed my indices such that the minimum hamming distance…

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Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

Orr, H. A. The genetic theory of adaptation: A brief history. Nat. Rev. Genet. 6, 119–127 (2005). Article  CAS  PubMed  Google Scholar  Dillon, M. E. & Lozier, J. D. Adaptation to the abiotic environment in insects: the influence of variability on ecophysiology and evolutionary genomics. Curr. Opin. Insect Sci. 36,…

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How to install bbmap on Ubuntu 20.04 (Focal Fossa)?

Quick installation of bbmap Architecture: all Version: 38.79+dfsg-1: Step 1: Update system: sudo apt-get update Step 2: Install: bbmap Architecture: all Version: 38.79+dfsg-1 Ater updaing the OS run following command to install the packae: sudo apt-get install bbmap Architecture: all Version: 38.79+dfsg-1 Package Details Package: bbmap Architecture: all Version: 38.79+dfsg-1 Version: 38.79+dfsg-1 Maintainer: Ubuntu Developers Home page: sourceforge.net/projects/bbmap/…

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BAM file read stats (A/T/C/G/ins/del) for each base position

BAM file read stats (A/T/C/G/ins/del) for each base position 2 Hi all, I have a bunch of Oxford Nanopore reads with a reference fasta. Wondering if anyone knows of any software / packages that would create some kind of csv or txt file that takes each base position in the…

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Insert size is so small, good or bad?

Insert size is so small, good or bad? 1 If you have the average insert size is ~158 estimated using BBMap . While the read length from the fastq file is 150. so we paired reads length (2*150) This means the paired end reads overlap by too much. Is this…

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How to calculate GC content of reads that mapped to a specific gene?

How to calculate GC content of reads that mapped to a specific gene? 1 Hello, I aligned my data with STAR and I have the BAM files. I would like to calculate the GC content of reads that mapped to a specific gene. I have found this thread Gc Content…

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phylogeny – Variation in 16S rRNA between assemblers – how do I know which is real?

I have a low-diversity metagenome (~11 bins > 80% completion). Out of the bins, 3 are of interest to me. None of the lower-completion bins that can be identified are from the group of interest. So let’s call the bins of interest 1, 2 and 3. The raw reads had…

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The complete sequence of a human Y chromosome

Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article  ADS  CAS  PubMed  Google Scholar  Miga, K. H. et al. Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res. 24, 697–707 (2014)….

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Minimum length of reads

Minimum length of reads 1 I have used a trimmer to trim my reads, based on their qualities. My raw reads were 126- 150 bp. I did not set any minimum length to filter out short reads. Hence, I have reads as small as 0-4 bps in my processed file….

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Metagenomes Assembles Genomes from cultivated freshwater bacterial communities

This dataset represents 122 Metagenomes-Assembled Genomes (MAGs) that were reconstructed from 20 individual microcosms in the context of understanding microbial community assembly processes. The cultivation media consisted in Artificial Lake Water (ALW) enriched with glucose and cellobiose (See details in Le Moigne et al., 2023, Ecology). The microcosms (200 mL)…

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A genome catalogue of lake bacterial diversity and its drivers at continental scale

Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  Pernthaler, J. Competition and niche separation of pelagic bacteria in freshwater habitats….

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Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling

Coil implantation in fetal lambs We have complied with all relevant ethical regulations for animal testing. All procedures followed the Canadian Council on Animal Care guidelines and were approved by the University of Western Ontario Council on Animal Care (protocol 2010-257). Time-dated pregnant Dorset × Rideau Arcott ewes (gestational age 76 days,…

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Very low average coverage obtained

Dear All, I got the viral genome assembly using metaviral spade. Since this is a relatively new genome, I don’t have any closest proper reference. So I mapped my reads back to contigs to know the coverage using bbmap and got the following output: java -ea -Xmx21819m -Xms21819m -cp /Tools/bbmap/current/…

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What could be the rage for Average Coverage after Assembly

Dear all, I performed viral genome assembly using metaviral spade and I wanted to map my reads back to contigs to know the coverage. I used bbmap for this purpose and got the following output: NOTE: Deleting contents of ref/genome/1 because reference is specified and overwrite=true NOTE: Deleting contents of…

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bbsplit running slow or out of memory?

bbsplit running slow or out of memory? 1 Hello, I have Illumina fastq files from some RNA-seq, ATAC-seq and WES that originated as PDX samples. I am looking to filter out contaminating mouse reads from the human reads in these datasets. I have used Xenome before but wanted to try…

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bbmap split paired-end reads back into separated fastq files?

bbmap split paired-end reads back into separated fastq files? 1 Hi, I am trying to remove human reads from my metagenomic sequences (skin samples). I have used the command recommended in the bbmap documentation: bbmap.sh minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/path/to/hg19masked/ qtrim=rl trimq=10 untrim -ea -Xmx100g in=reads.fq outu=clean.fq…

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BBDuk Guide – DOE Joint Genome Institute

“Duk” stands to Decontamination Using Kmers. BBDuk was made to combine many common data-quality-related trimming, filtering, and masking actions into an single high-performance tool. It are capable of quality-trimming or filtering, adapter-trimming, contaminant-filtering via kmer matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation, subsampling, quality-score recalibration, kmer…

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Use bbmap reformat.sh to convert from paired fq files to a bam file

Use bbmap reformat.sh to convert from paired fq files to a bam file 1 As outlined here I was able to create paired-end fastq files with the help of GenoMax . Now I wonder how I can use reformat.sh from bbmap to convert this files to a valid bam file…

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Use bbmap reformat.sh to convert from paired fq files to a valid abam file

Use bbmap reformat.sh to convert from paired fq files to a valid abam file 1 As outlined here I was able to create paired-end fastq files with the help of GenoMax . Now I wonder how I can use reformat.sh from bbmap to convert this files to a valid bam…

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randomreads.sh only produces reads for chr1 to chr7

randomreads.sh only produces reads for chr1 to chr7 0 I used randomreads.sh from bbmap to generate reads from a fasta file generated with FastaAlternateReferenceMaker from GATK. It seems no matter which options I choose the script stops generating reads and chromosome 7 despite the fasta file contains all contigs from…

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Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

Sample collection Sampling kits were sent out to various bat rehabilitators in the UK, as described previously56, for the collection of faeces from bats. These faecal samples (0.02–1 g) were immediately stored in 5 ml of RNAlater solution to prevent degradation of RNA. The geographical locations and collection dates for all samples…

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RCAC – Knowledge Base: Biocontainers: bbtools

bbtools Link to section ‘Introduction’ of ‘bbtools’ Introduction BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. Docker hub: hub.docker.com/r/staphb/bbtoolsHome page: jgi.doe.gov/data-and-tools/software-tools/bbtools/ Link to section ‘Versions’ of ‘bbtools’ Versions 39.00 Link to section ‘Commands’ of ‘bbtools’ Commands Xcalcmem.sh a_sample_mt.sh addadapters.sh addssu.sh…

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bbduk.sh trimmer with multiple input files

bbduk.sh trimmer with multiple input files 0 Hi all, I am using bbduk.sh and was wondering if there’s an efficient way to process multiple sets of reads with it? E.g. if you have read 1 as 4 separate files and read 2 as 4 separate files, typical mappers like bowtie2…

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[Detailed Question] How to Normalize of Metagenomics Gene Abundances (with HMMs models)

Hi everyone, Me and my colleagues have been thinking about normalization for quite some time, and we have a hard time finding a consensus both within us, and within the literature, for this reason, this is going to be a long and detailed post. Talking with other researchers we feel…

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Error with dada2 while running Parkinson’s Mouse Tutorial – Technical Support

Hi, everyone. I’m new to qiime2 and I have a technical issue. I have the same problem with forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-255/21016 when I ran Parkinson’s Mouse Tutorial, but I noticed the problem didn’t solved in the website above.That’s my error info: Plugin error from dada2: An error was encountered while running DADA2…

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Distribution and diversity of ‘Tectomicrobia’, a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites

Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143–69. CAS  PubMed  PubMed Central  Google Scholar  Konstantinidis K, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017;11:2399–406. PubMed  PubMed Central  Google Scholar  Parks…

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Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range

Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, et al. The population biology of invasive species. Annu Rev Ecol Syst. 2001;32:305–32. Article  Google Scholar  Allendorf FW, Lundquist LL. Introduction: population biology, evolution, and control of invasive species. Conserv Biol. 2003;17:24–30. Article  Google Scholar  Erickson AB. The…

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An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…

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BBduk reading fastq from S3 directly

BBduk reading fastq from S3 directly – Is it possibile? 0 Hello to all, I am not from Bioinf field but there is no issue for me running bbduk trimming command 🙂 I was wondering is it possibile to load paired fastq reads directly form S3 bucket? Even better, load…

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BBmap params for accurate MAG relative abundance estimation?

hi folks, Recently, I’ve been working on developing molecular and computational methods to improve the accuracy of relative abundance estimation of metagenome assembled genomes (MAGs) from NGS datasets. Most of this work is focused on host-associated viral metagenomics, where quite a bit of nucleic acid manipulation and amplification is needed…

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Normalizing before Metaphlan2

Normalizing before Metaphlan2 1 Hello, I am had run Metphlan2 to understand the relative abundance of some organisms in three of my samples. I have differences in the number of reads in the samples after Quality control. Do I need to normalizing the reads? Will normalizing the reads with depth…

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Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells

scEC&T sequencing A detailed, step-by-step protocol of scEC&T-seq is available on the Nature Protocol Exchange46 and is described below. The duration of the protocol is approximately 8 days per 96-well plate. Cell culture Human tumor cell lines were obtained from ATCC (CHP-212) or were provided by J. J. Molenaar (TR14; Princess…

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BBduk log and stats appear to be inconsistent

BBduk log and stats appear to be inconsistent 0 Hi All, I’m using BBduk to filter out reads where there is a kmer match to a specific set of contaminant sequences. Here is an example command: bbduk.sh \ in1=${FQ1} \ in2=${FQ2} \ ref=${contaminant_fasta} \ k=21 \ hdist=1 \ stats=${OUTPUT}/${SAMPLE}_stats.txt \…

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Question on removing duplicates with ATAC-Seq and ChIP-Seq

Question on removing duplicates with ATAC-Seq and ChIP-Seq 0 Hi I am new to ATAC-Seq and ChIP-Seq and I have a question on removing duplicates when it comes to paired-end ATAC-Seq and paired-end ChIP-Seq pipelines. I have seen some papers where clumpify is used in the first step to remove…

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NGS demultiplexing

NGS demultiplexing 1 Hello everyone, I am working on a linkage project for Sars COV-2. I used Illumina iseq1000 for sequencing. The indexes I use for the study are designed as 10bp, but they were entered as 8bp during the operation of the device. When I demultiplex with bcl2fastq, all…

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Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge

Baumgart, D. C. & Sandborn, W. J. Inflammatory bowel disease: Clinical aspects and established and evolving therapies. Lancet 369(9573), 1641–1657 (2007). Article  CAS  PubMed  Google Scholar  Baumgart, D. C. The diagnosis and treatment of Crohn’s disease and ulcerative colitis. Deutsches Aerzteblatt Online 106(8), 123–133 (2009). Google Scholar  Conrad, K., Roggenbuck,…

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Biogeographic patterns of biosynthetic potential and specialized metabolites in marine sediments

Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006;4:102–12. Article  CAS  PubMed  Google Scholar  Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol. 2012;10:497–506….

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Supported Tools – MultiQC

Tool Tool Name Description Removes adapter sequences and trims low quality bases from the 3′ end of reads. Overlapping paired-ended reads can be merged into consensus sequences and adapter sequence can be found for paired-ended data if not known. Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data….

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Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms

Novel Roseobacter strains isolated from marine biofilms We isolated and cultured bacterial strains from biofilms on natural rocks immersed in coastal waters. After preliminary analyses of 16S rRNA gene sequences generated by Sanger sequencing, more than 500 non-redundant strains were identified, including 54 distant strains affiliated with Roseobacter (hereafter referred…

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Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article  CAS  PubMed  PubMed Central  Google Scholar  Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…

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The persistence and stabilization of auxiliary genes in the human skin virome | Virology Journal

Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66. Article  CAS  PubMed  Google Scholar  Suttle CA. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12. Article  CAS  PubMed  Google Scholar  Breitbart M. Marine viruses: truth or dare. Ann…

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Hard clip fastq

Hard clip fastq 2 I hope this is not a silly question. I have 2x 200bp fastqs generated from MGI G400 sequencer. I would like to do a comparison with Illumina but these only come as 2x 150bp fastqs. Is it possible to hard clip the 2x 200bp fastqs down…

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error bbduk

error bbduk 0 Can anyone help me, I try to run the command and it gives this error, how can I adjust? java -ea -Xmx-78m -Xms-78m -cp /home/qiime2/Documents/bbmap/current/ jgi.BBDuk in= /Home/Desktop/Documents/limpeza/S2500_1.fastq out= /Home/Desktop/Documents/limpeza/S2500_1.fastq.clean.fastq trimq=20 minlen=75 Invalid maximum heap size: -Xmx-78m Error: Could not create the Java Virtual Machine. Error: A…

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Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?

Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding? 9 Is there a simple tool I can use to quickly find out if a FASTQ file is in Sanger or Phred64 encoding? Ideally something that tells me ‘Encoding XX’ somewhere the terminal output. fastq tools • 46k…

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A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes

Inagaki, F., Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing e-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 1801–1805 (2003). Article  CAS  PubMed  Google Scholar  Timmer-Ten Hoor, A. A new type of…

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ATAC-seq fragment size distribution – huge spike at 150 bp

HI, I am working on some ATAC-seq data. We have performed paired-end sequencing with read length of 150 bp on a total of 24 samples (8 conditions in triplicates) To begin with, I will just briefly describe some of the main analysis steps. I have trimmed the read to remove…

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Discovery and comparative genomic analysis of a novel equine anellovirus, representing the first complete Mutorquevirus genome

Manzin, A., Mallus, F., Macera, L., Maggi, F. & Blois, S. Global impact of Torque teno virus infection in wild and domesticated animals. J. Infect. Dev. Countries 9, 562–570 (2015). Article  CAS  Google Scholar  Biagini, P. et al. Family Anelloviridae. In Virus Taxonomy: Ninth Report of the International Committee on…

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RNA-Seq analysis using STAR and Salmon

RNA-Seq analysis using STAR and Salmon 2 Hello! I am having some trouble figuring out how to use Salmon. I have around 30 different samples which I trimmed using bbmap then aligned them using STAR. I have all of the BAM files from this alignment. Should I merge them all…

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BBMap’s repair.sh swaps sequences between input files

This is a bit of an XY problem but please go with it just for now. I have 10X scRNAseq I1, I2, R1 and R2 files. From these, I have extracted a subset of R2 reads into a subset.R2 file. I’ve also used filterbyname.sh to extract the same named subset…

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BBMap/sh/repair.sh not finding pairs

BBMap/sh/repair.sh not finding pairs 0 Hi, I am a beginner bioinformatician, I have paired-end fastq.gz files (file1 for R1 and file2 for R2) from illumina. I want to use these files for downstream analysis but I cannot because they don’t have the same number of reads. (the difference between read…

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How To Install bbmap on Ubuntu 20.04

In this tutorial we learn how to install bbmap on Ubuntu 20.04. bbmap is short read aligner and other bioinformatic tools b5833726e45421cf74f3885c83040a6f Introduction In this tutorial we learn how to install bbmap on Ubuntu 20.04. What is bbmap bbmap is: BBMap: Short read aligner for DNA and RNA-seq data. Capable…

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rRNA decontamination of RNA-Seq reads (tool choice, introns etc)

Greetings! I need some help with performing my rRNA decontamination step properly, which is part of pre-processing pipeline for my Illumina RNA-Seq reads, before mapping to the reference genome (a plant species). SOME RELEVANT LINKS AND MY CRUDE INFERENCES: Download Rrna Sequences – SILVA database is useful for human research,…

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Question about RNA-Seq data alignment

Question about RNA-Seq data alignment 3 Hi, I have a question about genome alignment. I am working with RNA-Seq dataset to study the impact of Liquid Culture in response to virus of different doses in Human. I was exploring what could be the good strategy or best in practice method…

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Mapping with bbmap.sh

Mapping with bbmap.sh 1 Hello everyone Todat I’m trying to do a mapping with bbmap but I have a problem because in the results I have NaN% in everything, this is normal? I’m using Ictalurus punctatus genome reference but my sample is pimelodus grosskopfii. In the picture you can see…

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calctruequality in bbmap

calctruequality in bbmap 1 I’m trying to recalibrate Q scores of a NextSeq run using MiSeq contigs assembled with Tadpole. The commands I used to map the reads to the reference were as follows: bbmap.sh in=concatABC.fastq.gz outm=mapped.sam ref=./Lpe09_06TdpAssemblies/contigs09_06.fa ignorequality maxindel=100 minratio=0.4 ambig=toss qahist=qahist_raw.txt qhist=qhist_raw.txt mhist=mhist_raw.txt The command I used to…

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command line – how to change name of multiple files at the same time

command line – how to change name of multiple files at the same time 2 Hi everyone, in a directory, I have several files named something like: Ricxxx_genomic.fna_0.97_bbmap_stats.txt Ricxxx_genomic.fna_0.97_bs.sh Ricxxx_genomic.fna_0.97_mapped.sam Ricxxx_genomic.fna_0.97_mapped_sorted.bam Ricxxx_genomic.fna_0.97_mapped_sorted.bam.bai and i would like to change their names to: p100e_Ricxxx_genomic.fna_0.97_bbmap_stats.txt p100e_Ricxxx_genomic.fna_0.97_bs.sh p100e_Ricxxx_genomic.fna_0.97_mapped.sam p100e_Ricxxx_genomic.fna_0.97_mapped_sorted.bam p100e_Ricxxx_genomic.fna_0.97_mapped_sorted.bam.bai What command line can…

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nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs | BMC Bioinformatics

Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci. 1976;73(11):3852–6. doi.org/10.1073/pnas.73.11.3852. Article  CAS  Google Scholar  Arnberg AC, Van Ommen G-JB, Grivell LA, Van Bruggen EFJ, Borst P. Some yeast mitochondrial RNAs…

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new module: bbmap/filterbyname – PullAnswer

new module: bbmap/filterbyname – PullAnswer Is there an existing module for this? [X] I have searched for the existing module Is there an open PR for this? [X] I have searched for existing PRs Is there an open issue for this? [X] I have searched for existing issues Are you…

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BBmap bbduk.sh for filtering reads

I’m looking to filter reads that contain a stretch of A’s, I found these posts looking for polyA tails, meaning this should work all the same (Identify RNA-seq reads containing polyA sequence, Identifying RNA-seq reads containing polyA stretch). However, I cannot get it to work. Given just these two reads,…

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Genetic characterization of two G8P[8] rotavirus strains isolated in Guangzhou, China, in 2020/21: evidence of genome reassortment | BMC Infectious Diseases

Mokomane M, Kasvosve I, Melo Ed, Pernica JM, Goldfarb DM. The global problem of childhood diarrhoeal diseases: emerging strategies in prevention and management. Ther Adv Infect Dis. 2018;5(1):29–43. PubMed  Google Scholar  Organization WH. Rotavirus vaccines: WHO position paper–July 2021. Weekly Epidemiol Rec. 2021;96(28):301–219. Google Scholar  Bucardo F, Reyes Y, Svensson…

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bgzf_read_block] EOF marker is absent reformat.sh

BBMap/BBTools reformat.sh : real error or spurious message? [W::bgzf_read_block] EOF marker is absent reformat.sh 1 When subsampling paired-end .fastq.gz files using reformat.sh from BBMap/BBTools, I get this error message: [W::bgzf_read_block] EOF marker is absent reformat.sh I’ve checked the input files with gunzip -t, no error. The input files are a…

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BBMap 38.90-GCC-10.2.0 (for BlueBEAR, BEARCloud VMs, and CaStLeS VMs)

BBMap 38.90-GCC-10.2.0 Unsupported: Use of this version of BBMap is not supported. More information on our Applications Support and Retention Policy. BBMap short read aligner, and other bioinformatic tools. Accessing BBMap 38.90-GCC-10.2.0 To load the module for BBMap 38.90-GCC-10.2.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs,…

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[W::bgzf_read_block] EOF marker is absent in BBMAP

[W::bgzf_read_block] EOF marker is absent in BBMAP 0 Hello, I’m asking an issue encountered in bbmap. I was using bbmap to remove host contaminants from my microbiome data. The commands are simple as below (ref folder already generated in the last step) bbmap.sh -Xmx42g in=R1.fastq.gz in2=R2.fastq.gz outu=cleaned.interleaved.fastq.gz threads=12 overwrite=t unpigz=t…

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