Question: Extract Spliced Transcripts From Cuffmerge
0
gravatar for Hanson, Sara J
6.1 years ago by
Hanson, Sara J10 wrote:
Hi All, I have mapped RNA-Seq reads to an unannotated partial genome assembly and assembled them into transcripts using the Tuxedo pipeline. II have used the "Extract Genomic DNA" tool to pull the annotated genes out of the genome assembly, but I would like the spliced transcripts as well. Is there a tool or pipeline that can retrieve the exons individually and concatenate them if they are part of the same gene? Any help on this would be much appreciated. Thanks!
assembly • 879 views
ADD COMMENTlink modified 6.1 years ago by Jennifer Hillman Jackson25k • written 6.1 years ago by Hanson, Sara J10
0
gravatar for Jennifer Hillman Jackson
6.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Sara, Starting with the assembled transcripts GTF file from Cufflinks, the following will pull out complete fasta records for each: 1 - "Filter and Sort -> Filter" using condition " c3!='transcript' " This removes lines that are technically out of spec for GTF format (thanks goes to Jeremy for the workaround). 2 - Send the resulting filtered GTF file to the "Fetch Sequences -> Extract Genomic DNA" tool and use the options 'Interpret Features' = True and 'Output data type' = Fasta Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENTlink written 6.1 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour