Extract Spliced Transcripts From Cuffmerge

Heads up! This is a static archive of our support site. Please go to help.galaxyproject.org if you want to reach the Galaxy community. If you want to search this archive visit the Galaxy Hub search

Latest

Open

RNA-Seq

ChIP-Seq

SNP

Assembly

Forum

Planet

All »

Home

Welcome to Galaxy Biostar! User support for Galaxy! about • faq • rss

Community

Log In

Sign Up

Add New Post

Question: Extract Spliced Transcripts From Cuffmerge

6.3 years ago by

Hanson, Sara J • 10

Hanson, Sara J • 10 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 • 934 views

ADD COMMENT • link •

modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Hanson, Sara J • 10

6.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »