gpertea
Questions concerning implementation of -i option
The -i option reads: "keep merged transcripts with retained introns (default: these are not kept unless there is strong evidence for them)." I have several questions about how StringTie2 handles this option.
(1) What rule does StringTie2 apply to determine whether evidence for an intron is sufficiently "strong" during merging of assembled GTFs? Is it looking for presence of the intron in a minimum number of samples whose GTFs are being merged? (2) If -i is used in conjunction with other options for merging (e.g., -T 1, -f 0.05), what is the impact on the merged gtf? Are the other options applied to the transcript isoforms with introns so that any that have been kept due to the -i would be removed for failing the others? Or is it the case that using the -i would lead to keeping transcript isoforms that would fail to meet the other two criteria?
