Cuffdiff is complaining about missing XS attribute about hisat2

[infphilo]

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?

[gdoura]

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

[infphilo]

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

[gdoura]

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