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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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Custom STAR indices #22

Closed riccardo-aiese closed 2 years ago

riccardo-aiese commented 2 years ago

Hello, I would like to try COMPSRA with some smallRNA-seq datasets I have from human samples. Since I already have STAR installed and a genome index generated, I was wondering if I can provide the STAR execution path and the index path to COMPSRA instead of installing them. Is this possible?

Thank you Riccardo

cougarlj commented 2 years ago

Dear riccardo-aiese,

I'm afraid not. In order to avoid some configuration issues, we fixed the directory for STAR. We will consider updating it in the next release. By the way, you can align the reads by STAR by yourself and run COMPSRA for the annotation part separately. You can take bam/sam file to COMPSRA as input when you running the annotation model.

Best Wishes, Jiang Li

On Fri, Aug 27, 2021 at 3:59 PM riccardo-aiese @.***> wrote:

Hello, I would like to try COMPSRA with some smallRNA-seq datasets I have from human samples. Since I already have STAR installed and a genome index generated, I was wondering if I can provide the STAR execution path and the index path to COMPSRA instead of installing them. Is this possible?

Thank you Riccardo

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riccardo-aiese commented 2 years ago

Dear Jiang Li, thank you very much for your feedback and for this nice tool! I was able to run COMPSRA with my previously made genome index by creating a softlink from my index directory to the COMPRSA "bundle_v1/db/star/" folder. Maybe this solution can be useful for other users as well.

Kind regards Riccardo

cougarlj commented 2 years ago

Dear riccardo-aiese,

Awesome, thanks! Your feedback is much appreciated. Thank you for using COMPSRA in your research.

Best Wishes, Jiang Li

On Sat, Aug 28, 2021 at 10:11 PM riccardo-aiese @.***> wrote:

Closed #22 https://github.com/cougarlj/COMPSRA/issues/22.

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