How To Make Use Of The Cufflinks Output In Further Analysis

Question

[Varun Gupta]

Hello

I am working on RNA-seq data and i used hg19 genome as reference. I used TOPHAT and generated accepted.hits.bam file.

I ran cufflinks onto it for transcript assembly differential expression. It generated 3 files namely

1.transcripts.gtf

2.isoforms.fpkm_tracking

3.genes.fpkm_tracking

I am interested in some of the genes whose genomic coordinates i have in bed format

Is it possible if i can extract those results from the files generated above for my list of genes.

Hope to hear from you guys soon

Regards

V

Answer 1

[JC]

Yes, you can do that. If your ran Cufflinks with an annotation GTF, the isoforms and genes files include the geneid and transcriptid, you can use your favorite parser to extract the data. Check the files descriptions in the Cufflinks website: http://cufflinks.cbcb.umd.edu/manual.html#cufflinks_output