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Tximeta for novel transcripts by stringite #68
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You'd want to check that these transcripts are both in the FASTA that you used to make a Salmon index (and hence in the Salmon quant files), and in the GTF. E.g.
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Hi Mike, thanks for your quick response. Yes, these novel transcripts are in the FASTA, the quant files and in the GTF:
I'm not sure if I might be missing something while importing the data. |
For example if you have Do you need to set this to |
Oh I also see a bigger problem. These transcripts are named differently in the FASTA/quant.sf and in the GTF.
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I am not getting your point; as for instance, in the examples that I provided, I see that the name of the transcript ID And you're right, the |
GTF doesn't have transcript ids of the form |
what about the following line of the GTF:
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Oh sorry you're right. I think I see what's happening. The code recognizes versions as numbers following the first One solution would be to fix this in the FASTA, just find replace This would not just help with tximeta but other tools that would recognize |
Ohh awesome! Ok, I will make those changes and re-run Salmon and then tximeta and will let you know how it goes (: thanks!! |
Hi Mike, Substituting Thanks a lot! |
Great, I will try to add this to the documentation. Thanks for the report. |
added this to the docs in b09fd02 |
Hello,
I am trying to run Swish on a novel transcript assembly. I tried to import some Salmon data using the gtf from novel transcripts that I obtained from StringTie. These novel transcripts have "MSTRG" as prefix. I import the data as following:
However, when I search for these novel transcripts, they seem to be missing.
I am using tximeta v1.14.1 and the R version 4.2.0 (2022-04-22).
Any help would be appreciated.
Thanks
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