filter_tx_by_intron_chain.py - reference annotation source can be 'none' so no filtering for gene type is performed

frattalab / PAPA

PAPA (Pipeline-Alternative Polyadenylation) - Snakemake pipeline for analysis of APA from short-read RNA-seq data

GNU General Public License v3.0

1 stars 0 forks source link

filter_tx_by_intron_chain.py - reference annotation source can be 'none' so no filtering for gene type is performed #17

Closed SamBryce-Smith closed 1 year ago

SamBryce-Smith commented 2 years ago

Would be nice to have the extra flexibility for users to provide their own set of transcripts. The act of comparing one set of transcripts to another is quite general and there may be use cases where reference set is not all annotated transcripts but already curated.

Alternatively, could also add options to specify the filtering column and key values. And toggle filtering on/off with an additional option. Maybe too complicated though.

related to #2

SamBryce-Smith commented 1 year ago

Closing as don't plan to use filter_tx_by_intron_chain.py further