How Can I See The Assembly Sequences In Cufflinks Output ?

Question

[ericismax12]

Hi,everyone.

I want to use RNA-seq data to find NATs,so I use tophat and cufflinks to map and assemble reads.

My question: Does cufflinks output can see the assembled sequences?

I only can see the exons start and end.

How can I get the assembled sequences? Thanks

Eric

Answer 1

[JC]

You can load the GTF file into the IGV browser (http://www.broadinstitute.org/igv/) or Savant browser (http://genomesavant.com/savant/) to see the assembled sequences by gene or transcript.

[Ram]

Hi JC, As I am also working in this area like your above answer!! Is it possible to get these assembled sequences in fasta file from cufflinks output??

[JC]

you can reconstruct each of them using the GTF coordinates and the genome reference.