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YangLab / CIRCexplorer2

circular RNA analysis toolset
http://circexplorer2.readthedocs.org/
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CIRCexplorer2 support for STAR paired-end reads #9

Closed iprada closed 7 years ago

iprada commented 7 years ago

Hi! As Tophat/Tophat-fusion has gone into a low maitenance period, it would be great to have an implementation that supports STAR aligned, paired-end reads.

Do you plan to have that in the future?

kepbod commented 7 years ago

Currently there is no big difference between parsing STAR aligned paired-end reads and single reads for CIRCexplorer2. The only issue is that CIRCexplorer2 could not use the information of mate reads to filter out false positives like Tophat. I will try to figure out how to further improving STAR parser in CIRCexplorer2 to support using those information.

kepbod commented 7 years ago

I have tested different cases how STAR outputs Chimeric.out.junction, and I found STAR reports chimeric junctions only when the mate read also supports this chimeric alignment. In other words, current version of CIRCexplorer2 could also be applied to STAR aligned, paired-end reads. I will update the documents later.

iprada commented 7 years ago

That sounds great! I woud run my samples trough it!