Question: why cuffmerge need a fasta sequence as running parameter
1
gravatar for ibphuangchen
3.5 years ago by
ibphuangchen10
United States
ibphuangchen10 wrote:

Hi there, --

I've got a question when I go through the tuxedo RNA-seq data processing, -- why cuffmerge need a fasta sequence as running parameter (i.e. "-s genome.fa") ?

I would imagine that what cuffmerge does is to further assemble transcripts that have been "preliminarily assembled' by cufflinks, by integrating all those transcripts.gtf files generated from cufflinks. GTF files have got all the genome coordinates information, and the resulted GTF file from cuffmerge has only output genome coordinates. So, why we need to put a fasta genome there when we run cuffmerge? 

Thanks in advance.

cuffmerge rna-seq assembly • 1.1k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by ibphuangchen10
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