Cufflinks output files

Question: Cufflinks output files

3.0 years ago by

contim • 0

United States

contim • 0 wrote:

I have performed Cufflinks on a TopHat file and obtain the 5 files without any error message.

However, when I inspect the output files (i.e. Cufflinks gene expression), the column gene_id and gene_short_name

are empty and only chromosome number and base number is given. What do I need to do to obtain a file with this additional information critical to evaluate the FPKM results?

Thank you

cufflinks • 1.5k views

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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by contim • 0

3.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Examine the reference annotation dataset being used or consider using one (GFF3 or GTF dataset).

There are specific attributes in reference annotation datasets that this tool package uses to populate these values with meaningful content. The idea is to make certain that the annotation is both an exact match for the reference genome used in the prior mapping step and that it contains those key attributes in order for the annotation to populate into the tool output. Full details here in the manual

If your genome is supported, the GTF from iGenomes can be used with the Tuxedo RNA-seq analysis tools (Tophat, Cufflinks, Cuffdiff, etc). The iGenomes genes.gtf dataset contains all of the extra attributes that enable full functionality. There are also other annotation sources depending on the genome.

Best, Jen, Galaxy team

ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you, I will try. Marco

From: Jennifer Hillman Jackson on Galaxy Biostar <notifications@biostars.org<mailto:notifications@biostars.org>> Reply-To: "galaxystar+820c2644+code@biostars.io<mailto:galaxystar+820c2644+code@biostars.io>" <galaxystar+820c2644+code@biostars.io<mailto:galaxystar+820c2644+code@biostars.io>> Date: Thursday, November 19, 2015 at 1:02 PM To: Marco Conti <marco.conti@ucsf.edu<mailto:marco.conti@ucsf.edu>> Subject: [galaxy-biostar] A: Cufflinks output files

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: Cufflinks output files<http: biostar.usegalaxy.org="" p="" 15081="" #15091="">:

Hello,

Examine the reference annotation dataset being used or consider using one (GFF3 or GTF dataset).

If your genome is supported, the GTF from iGenomes<http: support.illumina.com="" sequencing="" sequencing_software="" igenome.html=""> can be used with the Tuxedo RNA-seq analysis tools (Tophat, Cufflinks, Cuffdiff, etc). The iGenomes genes.gtf dataset contains all of the extra attributes that enable full functionality. There are also other annotation sources depending on the genome.

Best, Jen, Galaxy team

ADD REPLY • link written 3.0 years ago by contim • 0

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