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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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Paired end reads #18

Open Reksome opened 3 years ago

Reksome commented 3 years ago

I have two reads R1 and R2 for each sample. How to merge R1 and R2? As two different adapters were used for R1and R2, the QC has to be done seperately. The Alignment and Annotation step is not taking R1 and R2 for analysis. Please help

cougarlj commented 3 years ago

Dear Reksome,

COMPSRA is not designed for the paired-end data. If you insist on doing this, I think you may have to process R1 and R2 for each sample separately through all the pipeline.

Best Wishes, Jiang Li

mars188 commented 2 years ago

Ok, I have paired-end reads too. Can I combine (concatenate) the R1 and R2 into a single one read and then run COMPSRA on it?

mars188 commented 2 years ago

Here is the protocol that can be used for joining the R1 and R2.

https://github.com/HCGB-IGTP/XICRA

cougarlj commented 2 years ago

Dear mars188,

Yes, you can follow the pipeline using COMPSRA, but you have to remove the adapter separately before merging them (R1 and R2)together and put the longest read (or fake one) in the first line of the fastq file (COMPSRA will use the first line to decide the read length). I will think about to update this function in the future release.

Best Wishes, Jiang Li