[feature] add per-exon identity filter to collapse_isoforms_by_sam.py about cdna_cupcake

[qiuyixmm]

hello，
If i don't add --dun-merge-5-shorter parameter when run collapse_isoforms_by_sam.py, would the script collapse shorter 5' transcripts? If so, can it get the same results though i don't run filter_away_subset.py ? Thanks!

[Magdoll]

Hi @qiuyixmm ,

Very good questions and you are correct!

case 1:

collapse_isoforms_by_sam.py 

is equivalent to

case 2:

collapse_isoforms_by_sam.py --dun-merge-5-shorter
filter_away_subset.py

You may ask, why bother with --dun-merge-5-shorter then? It' because if then run get_abundance_post_collapse.py after the collapse step, the counts will be different. In case 1, the counts will include reads from both longer and shorter merged transcripts; in case 2; the counts will correctly reflect the longer and shorter as separate.

[qiuyixmm]

@Magdoll okay, it is vey kind of you to give me so detailed answer. Thanks!