Question: Transcripts ID matching in tximport for edgeR
0
gravatar for Sharon
2.7 years ago by
Sharon480
Sharon480 wrote:

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?

Thanks

edger rna-seq salmon tximport • 1.5k views
ADD COMMENTlink modified 2.7 years ago by WouterDeCoster44k • written 2.7 years ago by Sharon480
3
gravatar for WouterDeCoster
2.7 years ago by
Belgium
WouterDeCoster44k wrote:

Yes, safe.

You are looking for the ignoreTxVersion option of tximport:

logical, whether to split the tx id on the ’.’ character to remove version information, for easier matching with the tx id in gene2tx (default FALSE)

ADD COMMENTlink written 2.7 years ago by WouterDeCoster44k

Thanks a lot DeCoster. Works well now.

ADD REPLYlink written 2.7 years ago by Sharon480

You're welcome ron. Glad to help.

ADD REPLYlink written 2.7 years ago by WouterDeCoster44k
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