quantify
In your manual,flair quantify only needs 2 parameters: 1) the transcripts(.fasta) ; 2) the raw reads(.fastq). My questions are:
How did you assign the reads to transcripts? What alignment tool does flair quantify use? Is it still minimap2 in the flair align step? If so ,why not use the bam file directly?
The mapping quality of the raw reads are different. If flair quantify use raw reads directly while the bam files in the align step are filtered with mapping quality, then the reads are not matched between quantify step and identification step.
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
flair quantifyonly needs 2 parameters: 1)the transcripts(.fasta); 2)the raw reads(.fastq). My questions are:flair alignstep? If so ,why not use the bam file directly?flair quantifyuse raw reads directly while the bam files in the align step are filtered with mapping quality, then the reads are not matched between quantify step and identification step.Thank you！Looking forward to your reply!