Issue with Salmon and Deseq2 with paired-end and single-end reads libraries
0
0
Entering edit mode
22 months ago

Hi,

I have an issue regarding using Salmon and Deseq2 with mixed (paired-end and single-end) read libraries.

My libraries were originally paired end, but I quality-trimmed them, resulting in a lot of single-end reads that I don't want to throw away. I want to use Salmon to quantify expression. But since Salmon can't operate with both types of libraries at the same time, I ended up quantifying single- and paired-end reads separately, and then adding the read counts from same sample for each transcript.

salmon quantmerge --column numreads -o cohort95_nr_quant.sf --quants Sample*_quant 

python3 -c "
import pandas as pd
dfs=pd.read_csv('quants/cohort95_nr_quant.sf',sep='\t')
ndf=pd.DataFrame(columns=['Name'])
ndf['Name']=dfs['Name']
libs=['Sample'+str(num) for num in range(1,95)]
for lib in libs:
    ndf[lib]=dfs[lib+'.paired_quant']+dfs[lib+'.single_quant']
ndf.to_csv('quants/cohort95_summed_nr_quant.sf',index=False,header=True,sep='\t')
"

So I ended up with a file like:

Name    Sample1     Sample2     Sample3     ...
Transcript1     4811.874    11930.11    7938.97
Transcript2     34.0    79.0    104.0 
Transcript3     229841.3    262170.9    222405.4
Transcript4     0.0     11.0    6.0
Transcript5     0.0     0.0     0.0

Now I want to use Deseq2. I'm following the tximport tutorial for going from transcripts to genes, but I don't know how to use the file above. tximport() only takes original quant.sf files from salmon as long as I understand.

What can I do?

salmon deseq2 rnaseq tximport • 562 views
ADD COMMENT

Login before adding your answer.

Traffic: 2760 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6