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cougarlj / COMPSRA

COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis
https://regepi.bwh.harvard.edu/circurna/
GNU General Public License v3.0
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Question regarding circBase search by COMPSRA #58

Open zntaylgit opened 1 month ago

zntaylgit commented 1 month ago

How exactly does COMPSRA determine if a read maps to a circRNA? Does it specifically consider only reads that map to the splice junction? Otherwise, reads from linear mRNAs that map to an exonic sequence in the circRNA may erroneously be attributed to circular molecules, correct? Basically, I'm asking how the circBase database is employed in COMPSRA.

hadasvolk commented 6 days ago

@zntaylgit have you ever figured this out? I'm asking myself the same question

zntaylgit commented 6 days ago

@hadasvolk No, not yet; I've been working on other things. I haven't gotten a reply yet. If there is a way to run Compsra while saving each identified feature's reads, I was going use that and then blast all reads to a complete circRNA sequence to see if the splice junction was the only portion covered to any read depth. But its on the back burner, and I was hoping the author would save me the trouble by replying here. They are likely busy too though so I'm just sitting tight for the moment.

hadasvolk commented 4 days ago

@zntaylgit I think the code does not attempt to diffrentiate the mRNA and circRNA. I wonder why or where this claim that all those reads are circRNA originated from?!

zntaylgit commented 8 hours ago

@hadasvolk I'm not sure. Do they have code to create a replacement pre-built circRNA database I wonder?