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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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Annotation files numbers not matching Annotation report #21

Open yangtkc opened 3 years ago

yangtkc commented 3 years ago

Hello,

I just started using COMPSRA, and I noticed that the numbers shown in the annotation report (eg. number of annotated items covered by at least 1 read, or the number of reads that support annotation etc) don't match the numbers shown in the read count files. Could you explain to me the discrepancy?

Also, there are many unannotated items - is there a way to look at those when comparing two samples?

Thanks Christine

cougarlj commented 2 years ago

Dear yangtkc,

Thank you for using COMPSRA in your research. The annotation report is provided for each sample, but the count file is a summary of all samples. When merge these samples together, there are some integrating process. However, I think the discrepancy of count shouldn't be different significantly. If it does, please send me a real example and I can fix this potential bug.

To check the unannotated items, I remembered that I set a parameter "-asu" in the annotation model. So, you can add "-asu" after "-ann" and check the output.

Best Wishes, Jiang