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How Can I See The Assembly Sequences In Cufflinks Output ?

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

cufflinks
• 3,754 views • link
updated by Ram Ram • written by ericismax12 • ericismax12

1 answer

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.

• 1 views • link
written by JC JC

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??

• 0 views • link
written by Ram Ram

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

• 0 views • link
written by JC JC

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