Open akmazian opened 7 months ago
yup, just get your TCC matrix (omit --genecounts and put --multimapping to allow reads mapped to multiple genes to be preserved) and then run quant-tcc on the resulting matrix. This is basically the same as running kallisto for bulk RNA-seq (which gets you isoform-level quantification in an accurate probabilistic manner).
[update]: oops, I just realized you can use
kallisto quant-tcc
to do thisI know there are workarounds for this but it would be nice to have a
--transcript-counts
option forbustools count
that acts similar as--genecounts
:)Rationale:
Current workaround:
t2t.txt
file that maps each transcript to itself and use it in place oft2g.txt