Getting transcript abundace from StringTie merge gtf files

I am trying to determine the number of transcripts obtained from StringTie merge. The manual says to repeat the StringTie step using the merged file (which is a gtf file) but I can’t figure out how to do that on Galaxy.

Any ideas?

Thanks - Theo

Dear Theo,

Do you want to have the number of transcripts or the transcript abundance? These are two different things. The number of transcripts is well the number of transcripts :). Whereas the second is the estimation how often the transcript appears in your data, using an additional mapped read file in sam/bam format.

If you want the first one, then count the number of lines with “transcript” in your gtf file.

If you want the transcript abundance, then use the folowing tool: StringTie transcript assembly and quantification


I want the abundance of the reads defined by StringTie merge. The merge function eliminates the abundance data, and, if I understand the process correctly, the way to get abundance for merged transcripts is to do StringTie once again using these reads. The problem is that the output files from StringTie merge that I have are gtf files and I don’t know how to use them to do a second round of StrinngTie in Galaxy.

Thanks - Theo