Tag: BBMap

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…

Continue Reading new module: bbmap/filterbyname – PullAnswer

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,…

Continue Reading BBmap bbduk.sh for filtering reads

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…

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

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…

Continue Reading bgzf_read_block] EOF marker is absent reformat.sh

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,…

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

[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…

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

Feature count is very low using htseq-count

Feature count is very low using htseq-count 0 Hello all, I performed bbmap on my RNA-seq paired sequence data using following cmd bbmap.sh in1=J2_R1.fastq in2=J2_R2.fastq out=output_J2.sam ref=im4.fasta nodisk The header of generated sam file is @HD VN:1.4 SO:unsorted @SQ SN:k141_1006 LN:2503 @SQ SN:k141_5512 LN:5393 @SQ SN:k141_4772 LN:4387 @SQ SN:k141_3267 LN:4531…

Continue Reading Feature count is very low using htseq-count

BBTools – BioGrids Consortium – Supported Software

AllHigh-Throughput SequencingGenomicsProteomicsVisualizationOther BBTools Description a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. Installation Use the following command to…

Continue Reading BBTools – BioGrids Consortium – Supported Software

Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

Continue Reading Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

Continue Reading nf-core/circrna

Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings

Although the hypothesis of gene-regulatory network (GRN) cooption is a plausible model to explain the origin of morphological novelties (1), there has been limited empirical evidence to show that this mechanism led to the origin of any novel trait. Several hypotheses have been proposed for the origin of butterfly eyespots,…

Continue Reading Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings

Mapping to multiple references using bbmap

So my question comes in two parts: First of all is what I’m trying to do within reason given the tools I am using? I am investigating the shuffling effects of a recombinase on a known reporter sequence which subsequently generates libraries of unique sequences. By simulating all of the…

Continue Reading Mapping to multiple references using bbmap

Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

Continue Reading Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

Any alternatives to BBMap’s clumpify.sh program to optimize gzip compression?

Any alternatives to BBMap’s clumpify.sh program to optimize gzip compression? 1 I’ve had some difficulties implementing this in pipelines because it randomly fails sometimes. Are there any other programs that can be used in its stead? fastq genomics rnaseq • 201 views • link updated 7 hours ago by GenoMax…

Continue Reading Any alternatives to BBMap’s clumpify.sh program to optimize gzip compression?

Secret BBMAP helper page – HRGV/Marmics_Metagenomics Wiki

#How to map to the assembled scaffolds.fasta bbmap is a powerful and highly flexible read mapper jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/. For the upcoming analysis you are not interested in the typical mapping output but in statistics on the coverage on every scaffold, you can get them with scaffstats. We want to be specific…

Continue Reading Secret BBMAP helper page – HRGV/Marmics_Metagenomics Wiki

RNA-seq analysis cloud server

RNA-seq analysis cloud server 1 Hi all, I have some RNA-seq of mice (around 200GB) and I want to perform a RNA-seq analysis (including QC, mapping, quantification, differential expression analysis). But I don’t know how to choose a server. Could anyone can tell me to process such a dataset, how…

Continue Reading RNA-seq analysis cloud server

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

Continue Reading Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

is BBMap/Qualimap affected by log4j vulnerability

is BBMap/Qualimap affected by log4j vulnerability 2 no, unless the tools are used as a library in a web server. It’s worth noting picard.jar and abra.jar are affected (even though as Pierre L says, these are unlikely to be attacked on most systems). If you’re responsible for systems, esp web…

Continue Reading is BBMap/Qualimap affected by log4j vulnerability

Average Read length

Average Read length 3 Hello Everyone! Is there a standard tool commonly used to calculate the average read length of fastq files? If yes please mention it here because I want to know the size of average reads of my fastq files so that I can decide the cutoff for…

Continue Reading Average Read length

Single-cell delineation of lineage and genetic identity in the mouse brain

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

Continue Reading Single-cell delineation of lineage and genetic identity in the mouse brain

BBSplit ambiguous dataset analysis

BBSplit ambiguous dataset analysis 1 I have used bbsplit to split a metagenomic dataset into reads mapping to three genomes a, b, c. bbsplit.sh in1={fastq_1} in2={fastq_2} ref={ref_str} ambiguous2=split basename={out_path}out_split_%.sam If I want to identify which ambiguous reads align to ‘a’ and any other genome – is this only ‘ambiguous_a’? or…

Continue Reading BBSplit ambiguous dataset analysis

Trying to trim last bp of several samples with BBduk at once

Trying to trim last bp of several samples with BBduk at once 1 Hi, I am trying to use BBduk to trim back my 151bp sequences to 150bp. I tried to create a loop for this so I could do one entire pool at the time, but I do not…

Continue Reading Trying to trim last bp of several samples with BBduk at once

Count 5’End Mapped To A Specific Genomic Position

Count 5’End Mapped To A Specific Genomic Position 7 I got several SAM/BAM files, and I am interested in 5’ends of the mapped reads. Is there any tools or scripts to count how many 5’ends are mapped at a specific genomic position? N.B. I am not try to count the…

Continue Reading Count 5’End Mapped To A Specific Genomic Position

bbduk can’t read file

bbduk can’t read file 0 Hi all, When trying to filter reads using bbduk, I get the following error message: maskMiddle was disabled because useShortKmers=true Exception in thread “main” java.lang.RuntimeException: Can’t read file ‘/home/bioinf/TrainingData/SRR6197336/SRR6197336_1.fastq’ at shared.Tools.testInputFiles(Tools.java:185) at jgi.BBDuk.<init>(BBDuk.java:912) at jgi.BBDuk.main(BBDuk.java:78) This is my code: ~/Downloads/bbmap/bbduk.sh in1=~/TrainingData/SRR6197336/SRR6197336_1.fastq in2=~/TrainingData/SRR6197336/SRR6197336_2.fastq out1=~/TrainingData/reads/bbduk/SRR6197336_1_bbduk.fastq out2=~/TrainingData/reads/bbduk/SRR6197336_2_bbduk.fastq ktrim=r…

Continue Reading bbduk can’t read file

Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova

Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…

Continue Reading Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova

Plot LFC with pheatmap of differentially expressed gene list from DESeq2.

Hi, all! First post, so apologies for any flaws with post structure. I am attempting to make a basic heatmap that shows the log fold change of differentially expressed genes, as identified by DESeq2. See below the code I am using for DESeq2: ##Load DESeq2 source(“https://bioconductor.org/biocLite.R”) biocLite(“DESeq2”) biocLite(“stringi”) biocLite(“MASS”) install.packages(“survival”)…

Continue Reading Plot LFC with pheatmap of differentially expressed gene list from DESeq2.

Do you need a deduplication tool for FASTQ data in fastp?

Forum:Do you need a deduplication tool for FASTQ data in fastp? 2 Hi, I am the author of fastp, a tool to provide ultra-fast all-in-one FASTQ preprocessing functions. This tool has received 500+ stars in github (github.com/OpenGene/fastp), and has been cited for 40+ times since its paper published in Bioinformatics…

Continue Reading Do you need a deduplication tool for FASTQ data in fastp?

Linearize fasta files

Program versions used: BBMap – v. 38.32Seqtk – v. 1.3-r106Seqkit – v. 0.8.1Perl – v. 5.16.3Python – v. 3.6.6sed – v. 2.2.2 $ time (cat Homo_sapiens.GRCh38.dna.primary_assembly.fa > /dev/null) real 0m1.050s user 0m0.002s sys 0m1.045s With BBMap – reformat.sh $ time reformat.sh -Xmx40g in=Homo_sapiens.GRCh38.dna.primary_assembly.fa fastawrap=0) java -ea -Xmx40g -cp bbmap/current/ jgi.ReformatReads…

Continue Reading Linearize fasta files

Split fastq according to barcodes

Hello, everyone: I’m recently analyze my scRNA-seq data, the first step is to splitting fastq files according to my barcode file which looks like this: sc1 AACGTGAT sc2 AAACATCG sc3 ATGCCTAA sc4 AGTGGTCA sc5 ACCACTGT sc6 ACATTGGC sc7 CAGATCTG sc8 CATCAAGT sc9 CGCTGATC sc10 ACAAGCTA sc11 CTGTAGCC sc12 AACGCTTA My…

Continue Reading Split fastq according to barcodes