Tag: BBDuk

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…

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/…

Hello, We sent our samples off for RNA exome sequencing. We normally do mRNA sequencing but our RNA was degraded so RNA exome sequencing was recommended. We used the TruSeq RNA Exome kit. I am encountering issues I haven’t experienced before when trimming reads. Below is the adapter content from…

Cell culture All cell lines used and derived by different approaches in this study are listed in Supplementary Table 1. Detailed information about the experimental design, materials and reagents is presented in the Reporting Summary. Primary human adult dermal fibroblasts (HDFa) from three different female donors were obtained from Gibco…

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,…

barcodes not show up in overrepresented sequences in FASTQC 1 So, I have a Ribo-seq experiment with multiple samples and for each sample there are two barcodes, supplied by the sequencing lab, like this one: TACTCATA+GCCACAGG I just ran the FASTQC on that bugger and it didn’t pop up as…

Bacterial strains and culture conditions Escherichia coli strain DH5α (Thermo Fisher) was used for the propagation of plasmids, whereas E. coli BL21 DE3 (Novagen) was used for the expression and purification of ResR/McdR protein. Mtb Erdman was obtained from Dr. Ramandeep Singh at THSTI, India, and Mtb H37Rv mc2 790242…

“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…

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…

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…

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…

Abstract Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein…

> My input “reference” kmer has a “C” at the 9th position, while the > reported matching kmers both have a “T” at that position. `maskmiddle` option is true by default as a result you see that base being “matched”. maskmiddle=t (mm) Treat the middle base of a kmer as…

Hi All, I’m trying to use BBduk to find and filter exact 18-mer matches in a contaminant fasta file from a set of input reads. BBduk reports that matches exist, however when I examine the reads that are supposed to include one or more kmers, I cannot find the matching…

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…

Hi I would like to use bbduk to replicate the command line flags used by trim_galore for EM-Seq (NEB). The bismark user guide recommends this for trim_galore –clip_R1 10 –clip_R2 10 –three_prime_clip_R1 10 –three_prime_clip_R2 10 Explanation of the trim_galore parameters –clip_R1 <int> Instructs Trim Galore to remove <int> bp from…

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 \…

For the initial test of this protocol, DNA extraction, PCR, Nanopore library preparation, Nanopore sequencing, and subsequent data analysis were conducted at sea aboard the R/V Atlantic Condor in August 2021 [26]. This investigational effort resulted in the sequencing and analysis of deep sea sediment samples within hours of their…

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…

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…

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…

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,…

Data collection Metagenomic project information was collected from the MGnify metagenomic database31. Currently (September 2021), microbiome data (sequence, taxonomic, and functional information, etc.) of 325,323 environmental samples can be found in this database. Often, microbes from similar ecological communities have been studied by different groups at different times and locations….

Sample preparation We ordered the GIAB samples from the Coriell Institute (NA24385, NIST ID HG002; NA24149, NIST-ID HG003 and NA24143, NIST-ID HG004). DNA concentration was measured by Qubit. The library was constructed according to Illumina TruSeq DNA PCR Free Library Prep protocol HT (Illumina Inc., San Diego, CA, USA) for…

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,…

First, trimming adapters is definitely necessary as they are essentially a form of contamination. For quality trimming and filtering I would highly recommend reading the following: Trimming of sequence reads alters RNA-Seq gene expression estimates Essentially they show that aggressive trimming is a problem. To quote from the Conclusions: The…

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…

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,…

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…

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…

Primers trimming from Illumina paired-end reads by BBDuk software 0 Hi, I’m dealing with Illumina amplicon data. I’d like to apply BBDuk to remove primers from the 5’end of my forward and reverse reads, but have a couple of questions. Could you help me please? How may i indicate in…

    Significance To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth…