pavanvidem / chira Goto Github PK

Hi Pavankumar,

Thank you for this program, it is nice to have a user friendly program available for completing analyses on RNA-RNA interaction datasets. So far there have been very few programs produced for this function.

I ran into 2 issues while running it:

First, I have been unable to find a GFF file that is correctly formatted that works on the chira_merge.py step. The 'whole_transcriptome.gff' file you provided with your tutorial works for mouse, but is there a repository I can download this file from for human?

Second, the chira_map.py step seems to run into issues in the newer releases of ChiRA (v1.4.3). From a fresh install using 'conda install -c bioconda chira', an error occurs that prevents completion of the step:
[16-12-2022 17:19:11] START: Write alignments to BED
[E::idx_find_and_load] Could not retrieve index file for 'outdirect/sorted.bam'
This error does not occur with an earlier version of ChiRA I tried (ChiRA v1.0.2).

Please let me know if you can help with these issue.

Thanks for your help!
Brandon