Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Should I use chrM,random and haploid fasta file to build hg19? mozart RNA Sequencing 7 04-18-2013 12:07 AM
Tophat - aligning to known gene annotations whuzzy RNA Sequencing 0 02-09-2012 12:04 AM
tophat -G gene model annotations GTF format? silin284 Bioinformatics 15 04-21-2011 06:26 AM
tophat with a list of gene model annotations. fabrice Bioinformatics 2 10-13-2010 06:44 AM
TopHat GFF3 for UCSC Gene HG19 Bio.X2Y Bioinformatics 5 06-07-2010 12:43 PM

Thread Tools
Old 01-18-2011, 04:44 PM   #1
Location: Melbourne

Join Date: Dec 2010
Posts: 19
Default SpliceMap Gene annotations file for hg19


I'm using SpliceMap to identify novel exon junctions, but want to do all this on hg19. SpliceMap includes gene annotations for hg18 in example download, but not for hg19.

Is there a good way to get the annotations for Ensembl, RefSeq and knowngene for hg19 that will work with SpliceMap? (Just like the annotations in the example, except for being for the hg19 build.)

I can get the RefSeq ones working from the refFlat.txt file from UCSC, but haven't had any success with .bed annotation files I've tried to use that were downloaded from the UCSC table browser. (SpliceMap appears to mark almost all junctions as novel but when viewed in the UCSC browser they look well annotated.)

Thanks for your help,
trickytank is offline   Reply With Quote

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 05:41 PM.

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