Comments (4)
Hi @gdoura,
I think I just fixed this issue, but I'd like to make sure this fix indeed works on your case. Is there a way for you to provide me with splicesites.txt and a subset of the reads so that I can reproduce the issue and confirm that I fixed it correctly?
from hisat2.
Hi Kim,
thank you very much for your kind reply.
I have attached the splicesite.txt file below
splicesites.txt
as for the reads : I have worked with the Merkin datasets
for ex http://www.ncbi.nlm.nih.gov/sra?term=SRX196276
(hisat (-u1000) --sra-acc SRR594405 will be fine too)
Best
from hisat2.
I downloaded the SRA data, and ran HISAT2 using the same command on the data. I didn't get any spliced alignment without XS field. I also tested HISAT2 on both Mac and Linux systems. Would you like to check if this still happens when using the latest version of HISAT2 (v2.0.3)?
Thanks,
Daehwan
from hisat2.
Seems to be working with the new version indeed, I previously haven't done rigorous checking of which version either v2.0.2 and v2.0.3 I used to generate BAM files, seems that even --dta-cufflinks (or --dta) isn't needed any more for cufflinks to avoid throwing the XS warning message, it would be nice if we could retrieve the version of hisat2 used to generate a bam file. Thank you very much for your technical support.
Best
from hisat2.
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