how do you get all the potential processed transcripts

[pcantalupo]

Hello,

I'm trying to find novel transcripts so I don't use the -e option. Using the verbose option, I see in the output that it says

[10/07 16:20:42]^bundle NC_001538:1-5153 done (16 processed potential transcripts).

but it only outputs 7 transcripts in the GTF file. How do I get it to output all 16 potential transcripts? Thank you,

[mpertea]

There is no option in StringTie to output those extra potential "transcripts". Those 16 potential transcripts are just paths in the splicing graph that StringTie considers. In this case, once the reads are allocated to the top 7 transcripts there are not enough remaining reads to support the 9 other paths, and StringTie discards them.