Question: Salmon quant in Galaxy vs Command Line
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gravatar for NewtoBioinfo
3 months ago by
NewtoBioinfo0 wrote:

Hi All, I'm new to RNA-seq analysis and someone recommended that I do the quantification of my transcripts via Salmon before DGE analysis. I got the Salmon documentation and got the quant.sf files for samples using command line and then input that data into iDep tool for DE analysis. I also knew about Galaxy so I carried out the Salmon quant pipeline in Galaxy and fed the output into DESeq2. I realised that the DGE lists for the top 10 up/down-regulated genes were different in DESeq2 and iDep. I then fed the Salmon quant data from Galaxy into iDep into found different results to the previous analysis where the Salmon quant data had been obtained from command line. I know DESeq2 uses TPM data and iDep uses Read count data but the main thing I noticed was that the TPM and NumReads column values were not the same between the command line generated files and the Galaxy ones. I used the same transcriptome file for both Salmon quantifications. The bash for the command line was:

#!/bin/bash

for fn in *R1_001.fastq.gz

do

base=`basename $fn`;

samp=${base%_R1_001.fastq.gz};

echo "Processing sample ${samp}"

salmon quant -i Ovis_aries_index -l A -1 ${samp}_R1_001.fastq.gz -2 ${samp}_R2_001.fastq.gz 

-p 8 --validateMappings -o Salmon_output/quants/${samp}

done

Why am I getting different outputs between Salmon command line and Salmon on Galaxy?

rna-seq salmon • 179 views
ADD COMMENTlink modified 3 months ago by genomax91k • written 3 months ago by NewtoBioinfo0

For this to answer you have to show the code that Galaxy uses internally plus the versions of the tools on Galaxy and at your local machine. Is the index the same?

ADD REPLYlink written 3 months ago by ATpoint40k
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