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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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rlh parameter #26

Closed Ben7124 closed 2 years ago

Ben7124 commented 2 years ago

Hello,

I have a question about the rlh parameter to divide the reads into length intervals. I notice in the example rlh is 8,17. Does this mean only reads of length 8-17 are passed on to the next module? How to use this rlh parameter properly?

Thanks!

cougarlj commented 2 years ago

Dear Ben7124,

Thank you for using COMPSRA. The -rhl 8,17 will divide reads into 0-7,8-16 and >17 three groups. In default, the last group >17 will be used in the next step. If you use -rhl 17 and it will divide reads into <17 and >17 group and the >17 group will be used in default. If you want to choose the group by yourself, you can use the parameter in alignment module with -midx which takes 0 as the first group and 1 as the second group, but this only function when the module run together.

Thanks!