search

nanoporetech / pinfish

Tools to annotate genomes using long read transcriptomics data
Other
44 stars 13 forks source link

Question: minimum_isoform_percent #11

Closed martynakgajos closed 5 years ago

martynakgajos commented 5 years ago

What is the minimum isoform percentage parameter? And what does the value 1 mean: 1 as 1.0 (so 100%) or 1 as 1%?

bsipos commented 5 years ago

It's a percent, so it is 1%.

martynakgajos commented 5 years ago

And what does this parameter mean? What is it responsible for?

bsipos commented 5 years ago

It filters out isoforms with less that this percent of coverage at a "locus" (a group of transcripts starting roughly at the same position). Safe to set it to zero if worried about confusing your results.

defendant602 commented 4 years ago

@bsipos Could you please provide a recommended value for this parameter when annotating a genome using ONT cDNA data?

Thanks!