flair quantify

[ucsfpan]

I have read the paper (https://doi.org/10.1038/s41467-020-15171-6)
and the manual (https://flair.readthedocs.io/en/latest/) and I still have a question about

• quantify

• sample1 condition1 batch1 bc01_aligned_collapsed.fastq

flair quantify --reads_manifest reads_manifest.tsv --isoforms NC12878RNA_${samp}flair_collapse.isoforms.fa --threads 12 --tpm --quality 20 --output NC12878RNA${samp}
So how to use the quantify step? using bc01_aligned_collapsed.fastq from isoseq collapse or other fastq?

[cafelton]

Don't use the collapsed fastq, use the flnc reads if using PacBio data