Hi guys,
I run cuffdiff with an annotation file from Ensemble like this:
-------------------
cuffdiff -o diff_out -b ../genome.fa -p 8 -L s1,s2 -u genome.gtf tophat_s1/accepted_hits.bam tophat_s2/accepted_hits.bam
-------------------
where genome.gtf is Ensemble annotation file which has ~70000 different CDS annotation.
However in the output file of cds.fpkm.tracking, there are only ~14000 cds features. Why is that? Did I do anything wrong?
Any help is appreciated. Thank you so much.
Regards,
xiangq
I run cuffdiff with an annotation file from Ensemble like this:
-------------------
cuffdiff -o diff_out -b ../genome.fa -p 8 -L s1,s2 -u genome.gtf tophat_s1/accepted_hits.bam tophat_s2/accepted_hits.bam
-------------------
where genome.gtf is Ensemble annotation file which has ~70000 different CDS annotation.
However in the output file of cds.fpkm.tracking, there are only ~14000 cds features. Why is that? Did I do anything wrong?
Any help is appreciated. Thank you so much.
Regards,
xiangq
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