--mix with -e loses guide transcripts

[gpertea]

This issue is reproducible on the last test example:

stringtie --mix -e -G mix_guides.gff -o mix_e.out.gtf  mix_short.bam mix_long.bam

The output file has only 11 transcripts instead of the original 12 (isoform rna81953 is missing).

[bernardo-heberle]

Hi, I am curious about the progress on this issue.

I am running the following command on StringTie and getting the same kind of problem where many of the transcripts from the input annotation don't appear on the output.

stringtie $bam -p 16 -L -o "./${id}_${d}/${id}_${d}.transcripts.gtf" -v -e -G "${gtf}" -A "./${id}_${d}/${id}_${d}.gene_abund.txt" -C "./${id}_${d}/${id}_${d}.cov_refs.gtf"