Question: How Can I See The Assembly Sequences In Cufflinks Output ?
0
gravatar for ericismax12
8.5 years ago by
ericismax120 wrote:

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

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ADD COMMENTlink written 8.5 years ago by ericismax120
0
gravatar for JC
8.5 years ago by
JC12k
Mexico
JC12k wrote:

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.

ADD COMMENTlink written 8.5 years ago by JC12k

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??

ADD REPLYlink written 7.2 years ago by Ram150

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

ADD REPLYlink written 7.2 years ago by JC12k
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