Question: Cufflinks reports less transcripts then in gff
gravatar for grant.hovhannisyan
20 months ago by
grant.hovhannisyan1.7k wrote:

Hi Biostars,

To make transcriptome assembly, I mapped the reads (2x75, strand-specific, organism Candida albicans) with tophat2 and did assembly with cufflinks. The command line for the latter is

cufflinks --library-type fr-firststrand -o folder -g C_alb.gff -p 20 accepted_hits.bam

In final file genes.fpkm_tracking I have only 713 transcripts, while my gff contains around 6200 transcripts.

Option -g "Tells Cufflinks to use the supplied reference annotation a GFF file to guide RABT assembly. Reference transcripts will be tiled with faux-reads to provide additional information in assembly. Output will include all reference transcripts as well as any novel genes and isoforms that are assembled." So in theory in genes.fpkm_tracking I should observe all transcript from gff + new transcripts (if any).

Can somebody explain why I see less transcripts then in gff?

Thank you

cufflinks • 537 views
ADD COMMENTlink written 20 months ago by grant.hovhannisyan1.7k

Any previous exprerince with this issue?

ADD REPLYlink written 20 months ago by grant.hovhannisyan1.7k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 992 users visited in the last hour