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bioinfo-biols / CIRI-cookbook

Document for CIRI-series software
https://ciri-cookbook.readthedocs.io/en/latest/index.html
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Is CIRI2 or CIRIquant allowing for STAR-generated bam file? #25

Open lovebaboon1989 opened 1 year ago

lovebaboon1989 commented 1 year ago

Hi there, I'd like to try using CIRI2 or CIRIquant to map circRNA reads in human genome. But since my project has over 1000 samples and we've already done the alignment work for mRNA by STAR aligner (which took lots of time), so I just wonder whether these tools may allow for the STAR-generated BAM file as a input? Because if we rerun the genome alignment pipeline using bwa-mem once again, that could cost a lot of time.. Thanks a lot and looking forward to your kind reply! Best regards, Weiqian Jiang

Kevinzjy commented 1 year ago

Hi, @lovebaboon1989.

  1. CIRI2 could not use STAR-generated bam as output

  2. CIRIquant by default uses bwa-mem and CIRI2 to detect circRNAs from the sequencing reads, and the bam provided in the --bam option is used for FSJ reads detection. So unless you already generated the circRNA files using other circRNA tools, running bwa-mem and CIRI2 is inevitable.

As you already have STAR output, maybe you can run CIRCexplorer2 to detect circRNAs. Then you can still run CIRIquant with --circ CIRCexplorer2_output --tool CIRCexplorer2.

lovebaboon1989 commented 1 year ago

Hi Kevin, Thanks a lot for the explanation!