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LosicLab / starchip

Detection of Circular RNA and Fusions from RNA-Seq
http://starchimp.readthedocs.io/en/latest/
MIT License
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Issue with chimeric.out files #12

Closed RosannahCameron closed 6 years ago

RosannahCameron commented 6 years ago

Hi there,

I've just started using STARchip with the latest version of STAR (2.6.0a) and running into an issue as I don't seem to have a chimeric.out.sam file produced. I can generate the chimeric.out.sam with --chimOutType SeparateSAMold but then the chimeric.out.junctions file isn't created. I can run STAR twice to generate both files but I was wondering if there is a better solution?

kippakers commented 6 years ago

Hi Rosannah,

Thanks for using STARChip! Thanks also for bringing this to my attention--I hadn't seen this change yet. I don't see a better way at the moment, but I've put in a message to the STAR developer (here) , he may know a trick or be willing to implement an option for me. Otherwise, I'll have to implement some large-ish changes to STARChip. For now, I recommend running STAR twice, or using an older version of STAR.

Thanks, Kipp

kippakers commented 6 years ago

Looks like Alex has an updated STAR 2.6.0c with the ability to use the option: --chimOutType Junctions SeparateSAMold , which should solve your issue. Thanks again for bringing this to our attention!

RosannahCameron commented 6 years ago

Thanks for addressing this Kipp (and Alex)! Just a side note when I ran STAR twice to generate the junction and sam files I also needed to use sort the files with -V. I assume the fix you mentioned can generate two files that will be sorted the same way.