Tag: BBDuk

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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Should I trim adapter sequences and filter by phred score, before alignment by salmon? : bioinformatics

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…

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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…

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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,…

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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…

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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…

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Primers trimming from Illumina paired-end reads by BBDuk software

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…

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ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

    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…

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