Closed RosannahCameron closed 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
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!
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.
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?