I am using tximport to convert transcripts counts from Salmon to gene counts for edgeR. Here is how my Salmon counts look like:
Name Length EffectiveLength TPM NumReads NM_000014.5 4945 4714.81 16.5914 4870.8 NM_000015.2 1317 962.778 0.0333619 2 NM_000016.5 2623 1865.02 5.28102 613.276 NM_000017.3 1964 1925.07 1.67686 201
But my tx2gene is like that, with no version (.x) after the transcript id:
TXNAME,GENEID NM_130786,A1BG NR_015380,A1BG-AS1 NM_001198818,A1CF NM_001198819,A1CF NM_001198820,A1CF
tximport throws the following error :
None of the transcripts in the quantification files are present in the first column of tx2gene. Check to see that you are using the same annotation for both
My question is: Is it safe to remove the version .x numbers from my Salmon counts to match tx2gene file? The transcripts in Salmon will match tx2gene if I removed the version .x. Like for example convert NM_000014.5 in Salmon counts to NM_000014?