isoquant results

[Nikhilgunala]

hi @andrewprzh

command : isoquant.py -d pacbio_ccs --fl_data --bam minimap2mappedsorted.bam --reference chromosomes.fa --output isoquant --threads 8 --transcript_quantification all --gene_quantification all --matching_strategy precise

why in the final trsncript_model.gtf file , only nnic transcripts are reported, how to get all transcripts not only novel ??

results : 229730 exon 22475 gene 30210 transcript

thank you in advance !!

[andrewprzh]

Dear @Nikhilgunala

You are running IsoQuant in a annotation-free mode, thus every output transcript is classified as "novel not in catalog". IsoQuant needs a reference annotation (provided via --genedb) to detect known or "novel in catalog" transcripts.

Best Andrey

[Nikhilgunala]

thank you very much @andrewprzh

[Nikhilgunala]

Dear @andrewprzh

Please tell me, is there any way to count single exons also for pacbio flnc reads ??

thank you! Nikhil

[andrewprzh]

@andrewprzh

You may use --count_exons option, but in the current version it only works when the reference annotation is provided.

Best Andrey