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Is CIRCexplorer2 allowing for STAR-generated bam file as input? #64

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lovebaboon1989 opened this issue Jan 24, 2023 · 1 comment
Open

Is CIRCexplorer2 allowing for STAR-generated bam file as input? #64

lovebaboon1989 opened this issue Jan 24, 2023 · 1 comment

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@lovebaboon1989
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Hi there,
I'd like to try using CIRCexplorer2 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 CIRCexplorer series tools may allow for the STAR-generated BAM file as a input? Because if we rerun the genome alignment pipeline using pair-end fastq files once again, that could cost a lot of time..
Thanks a lot and looking forward to your kind reply!
Best regards,
Weiqian Jiang
@kepbod
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kepbod commented Jan 30, 2023

If you want to use BAM files from STAR alignment, it requires chimeric alignment (set --chimSegmentMin in STAR) for CIRCexplorer2 to identify circRNA junction reads.

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@kepbod @lovebaboon1989