SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat: generate junctions.bed file from BAM file Julien Roux Bioinformatics 5 01-14-2016 04:19 PM
RNA-STAR filter out unique Junctions frymor Bioinformatics 0 10-04-2015 10:20 PM
STAR vs TopHat viewing junctions biocomputer Bioinformatics 1 11-28-2014 12:45 AM
Generating genome with splice junctions - STAR shivshiv Bioinformatics 8 09-27-2014 03:21 AM
Export Annotated Splice Junctions from NCBI? twaddlac RNA Sequencing 0 02-22-2011 10:38 AM

Reply
 
Thread Tools
Old 12-15-2015, 08:24 AM   #1
lre1234
Senior Member
 
Location: US

Join Date: Aug 2011
Posts: 106
Default Annotated junctions file for STAR

Hi all,
Does anyone know where I would be able to get an annotated splice junction file that I could use with STAR? I've been searching for one, but have been having trouble trying to locate one. Also, I believe it should be created from a gff3 file, but am having a bit of trouble figuring out the conversion.

Thanks for you help
lre1234 is offline   Reply With Quote
Old 12-16-2015, 01:31 PM   #2
alexdobin
Senior Member
 
Location: NY

Join Date: Feb 2009
Posts: 161
Default

Quote:
Originally Posted by lre1234 View Post
Hi all,
Does anyone know where I would be able to get an annotated splice junction file that I could use with STAR? I've been searching for one, but have been having trouble trying to locate one. Also, I believe it should be created from a gff3 file, but am having a bit of trouble figuring out the conversion.

Thanks for you help
Hi @lre1234

you can feed a properly formatted GFF3 file directly to STAR with --sjdbGTFfile /path/to/annot.gff3 --sjdbGTFtagExonParentTranscript Parent , and STAR will extract the junctions from the file.
Another option is to convert GFF3 to GTF (for instance with Cufflinks utility gffread -T annot.gff3 -o annot.gtf) and then run STAR with simply --sjdbGTFfile /path/to/annot.gtf .

Cheers
Alex
alexdobin is offline   Reply With Quote
Reply

Tags
junctions, splice junction, star aligner

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:24 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO