Question: "found spliced alignment without XS attribute" while running cuffmerge
gravatar for arronar
4.8 years ago by
arronar200 wrote:


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
blah blah blah

Files i gave to it, first aligned with tophat2 and then assembled with stringtie. Any idea on why that error pops up ?

Thank you.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by arronar200

Assuming the file was produced/modified by stringtie, then that would seem to be a stringtie bug.

ADD REPLYlink written 4.8 years ago by Devon Ryan93k

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

ADD REPLYlink written 4.8 years ago by arronar200

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.

ADD REPLYlink written 4.8 years ago by Devon Ryan93k

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).

ADD REPLYlink written 4.2 years ago by 123jnoble1230
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