ChrUn important?

[JQL]

Hi,

I am running cufflinks for RNA-seq. When running cuffmerge and cuffdiff, I got many of these warning messages: couldn't find fasta record for 'chrUn_AAEX03023826.1'!

I work on canine transcriptome whose genome is not as well annotated as other organisms'. In genome fasta file (canFam3.fa), it has "chrUn", but in the ensembl gtf file, chrUn breaks down to many chrUn_AAEX... and chrUn_JH... I guess thats why cufflinks can't find the records.

Is chrUn less important? should I just ignore the warnings? otherwise, how to fix this?

thanks

[westerman]

Is chrUn less important?

Probably. And in general you'll be safe ignoring it since your science is likely to concentrate on the main part of the genome. On the other hand if your transcriptome is lighting up (i.e., expressing) parts of the chrUN and if you want to chase down that those parts do then you might have an interesting paper.

[JQL]

thank you for your comments.

The warning messages from chrUn didnt' seem to affect the analysis. Other chromosomes see all run fine.