Using Cufflinks with SRA Reads

Question

[bandanaschapagain]

Hie all, I am using cufflinks to get the expression value for my fasta datasets. I am using Helicobacter pylori J99 SRA reads with Helicobacter pylori J99 reference genome. I got four outputs from cufflinks as: 1.genes.fpkm_tracking 2.isoforms.fpkm_tracking 3.skipped.gtf 4.transcripts.gtf

From these four outputs I do not have idea to which one I should consider for getting expression values. For my project I do not have use cuff diff. It would be great help if anyone could help me with this. Regards, Bandana

[Ron]

Is this a "tutorial" or a "question"?

[WouterDeCoster]

Now it's a question.

Answer 1

[Ron]

For genes expression values : genes.fpm_tracking

For transcripts expression values : isoforms.fpkm_tracking

http://cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html#transcript-level-expression-isoformsfpkmtracking

[bandanaschapagain]

Thank you for the information. I apologize for my mistake above. I have a question, I have cuff merge output of a giant file from which I need to get the expression values. I have no idea which column to look for.If only I could get help for this.

Regards, Bandana

[Ron]

You need to look at FPKM column

http://cole-trapnell-lab.github.io/cufflinks/cufflinks/#gene-level-expression-genesfpkmtracking