Can PSI-Sigma accept bam file generated from other aligner like bowtie2 or hisat2?

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PSI-Sigma

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Can PSI-Sigma accept bam file generated from other aligner like bowtie2 or hisat2? #1

Closed xiekunwhy closed 5 years ago

xiekunwhy commented 5 years ago

Hi,

README tells me that PSI-Sigma use bam file generated from star, and I just want to known if PSI-sigma accept bam files generated from other aligners?

Best wishes, Kun

wososa commented 5 years ago

Hi Kun,

Sorry that I missed your comment. Currently, .bam and .SJ.out.tab files from STAR are preferred. .SJ.out.tab files from other alingers may have different formats. You will need to convert them to STAR's format. Bowtie2 doesn't generate junction-read files, so it is not compatible with PSI-Sigma.

Thanks, Woody