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Hi,
I ran the nf-core/rnaseq and DESeq2 with quant.sf files and tximport()
In the results files, I found the duplicated gene names which are seperated by '-2' such as AKAP17A / AKAP17A-2
So I checked the txi file and tx2gene file, and I identify the tx2gene.tsv file in star_salmon contains three columns.
In second column, there are some duplicated gene names separated by '-2'
I think when I create new tx2gene.tsv file by using first column and third column I can get results file with unique gene names
I'm just curious about the difference between second column and third column in tx2gene.tsv
Thank you
Hi,
I ran the nf-core/rnaseq and DESeq2 with
quant.sf
files andtximport()
In the results files, I found the duplicated gene names which are seperated by '-2' such as AKAP17A / AKAP17A-2
So I checked the txi file and tx2gene file, and I identify the
tx2gene.tsv
file in star_salmon contains three columns.In second column, there are some duplicated gene names separated by '-2'
I think when I create new tx2gene.tsv file by using first column and third column I can get results file with unique gene names
I'm just curious about the difference between second column and third column in
tx2gene.tsv
Thank you
here is my command
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