"found spliced alignment without XS attribute" while running cuffmerge
Hello!
I just came face to face with a problem when tried to run the cuffmerge to assembly results.
The error says:
SAM error on line 87398: found spliced alignment without XS attribute
...
Files I gave to it, first aligned with tophat2 and then assembled with stringtie. Any idea on why that error pops up?
Thank you.
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Assuming the file was produced/modified by stringtie, then that would seem to be a stringtie bug.
You mean stringtie's bug as application or the problem occurred from the way i run it?
The command i used is :
stringtie -G Genes/genes.gtf -o stringtie_output -p 3 tophat_output/accepted_hits.bam
As in a bug in stringtie itself. I don't use stringtie, so I don't know if it produces its own realigned BAM files (with cufflinks, that wouldn't be the case). If it does, then the problem is stringtie. If it doesn't, then the problem is with tophat2.
Hey arronar,
Did you ever find a solution to this problem. I am trying to merge stringtie & cufflinks via cuffmerge and encountered the same error(s).