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second and third columns meaning in tx2gene.tsv from star_salmon #1193

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jdanaK opened this issue Jan 16, 2024 · 0 comments
Open

second and third columns meaning in tx2gene.tsv from star_salmon #1193

jdanaK opened this issue Jan 16, 2024 · 0 comments
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@jdanaK
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jdanaK commented Jan 16, 2024

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

here is my command

sudo nextflow run nf-core/rnaseq \
--input samplesheet.csv \
--outdir outdir \
--genome GRCh38 \
-profile docker \
--pseudo_aligner salmon
@drpatelh drpatelh added the question Further information is requested label May 13, 2024
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