merge close circRNA - Githubissues

LosicLab / starchip

Detection of Circular RNA and Fusions from RNA-Seq

http://starchimp.readthedocs.io/en/latest/

MIT License

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merge close circRNA #21

Closed huangziyan11111 closed 5 years ago

huangziyan11111 commented 5 years ago

Hi, I have a question about the circRNAs with close position. in the paper you said: CircRNA reads passing these filters are then merged if junction ends are very close. while in the code,is this script starchip/scripts/circles/filter_circsv3.pl can fulfill this merge step? and which parameter can handle it?

kippakers commented 5 years ago

Hi, sorry this took so long to respond, I missed the notification!

This process is handled by merge_close_crna_1file.pl , it merges circRNA with the same chromosome, and the splice donor and splice acceptor are within 10bp. At the top of that script is a set parameter called $distancemax, you can change 10 to whatever value you want.

Cheers, Kipp