TMPcalculator mising genes and duplicating other genes

[valopes2019]

I am facing issues with TPMcalculator! First, I noticed that it is counting much less number of genes. Second, among the counted ones there are duplications (same gene_ID in two lines).

I've checked my gtf file and looks fine... What could it be?

[r78v10a07]

Could you share the two lines with the same gene, please?

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On Fri, Sep 25, 2020 at 7:14 AM valopes2019 ***@***.***> wrote: I am facing issues with TPMcalculator! First I noticed that it is counting much less number of genes and amount the counted ones there are duplications (same gene_ID in two lines). I've checked my gtf file and looks fine... What could it be? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#61>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACB6FODVJORZ2MPRNZRS5GDSHR3S7ANCNFSM4RZNL3GA> . --

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[valopes2019]

The gene duplicates problem is solved. It was the same gene ID in different locations. Which I found weird but it is like this in the gtf file. However, I have a total of 20700 genes and TPM results for 20695. I've used the -a parameter.
Any ideas of why I am missing these five genes?
Thank you!

[r78v10a07]

Hi,
Could you attach the GTF or send it as a M to me, please? I will check the genes that are missed.