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HCGB-IGTP / XICRA

Small RNAseq pipeline for paired-end reads
MIT License
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Compatibility with sRNAbench #43

Closed jonahcullen closed 7 months ago

jonahcullen commented 1 year ago

Hello, I had a question about using XICRA with sRNAbench.jar. I seem to be running into issues correctly parsing the output of with mirtop. I realize you are not the maintainer of either of these tools so I'm really just curious if you have also found similar problems or perhaps workarounds? From what I can tell, it looks like there might have been update to sRNAbench.jar that breaks mirtop gff from correctly parsing the isoLabel.

Thanks for your time, Jonah.

JFsanchezherrero commented 1 year ago

Hi there Jonah, Yeah, I am afraid, sRNAbench is no longer valid to be used within XICRA.

At the beginning we used it but it was updated (or depecrated..). Also, installing it is tedious and not 100% user-friendly.

Also, in the publication of XICRA, we tested using simulated reads the performance of miraligner, sRNAbenchand optimir, basically, the few software available with miRTop format availability. We found miralignerto be the best and we started using it as our default software.

We recently came across miRge3 but I have not tested yet,

Regards