SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
New Ribo-Zero Gold Kit (Human/Mouse/Rat) epibio Vendor Forum 7 08-01-2014 12:35 PM
Ribo-Zero (Human/Mouse/Rat) kit now in magnetic format epibio Vendor Forum 1 02-06-2012 06:48 AM
Graphical visualization of GFT files ccstaats Bioinformatics 2 02-01-2012 06:36 AM
Best annotated mamalian genome, excluding human/mouse/rat warrenemmett Bioinformatics 2 10-12-2011 02:08 AM

Reply
 
Thread Tools
Old 07-06-2011, 12:40 PM   #1
biofreak
Member
 
Location: USA

Join Date: Jun 2011
Posts: 44
Default GFT file for rat

I want to run tophat for rat samples. Where do I download the gtf file from?
thanks
biofreak is offline   Reply With Quote
Old 07-07-2011, 03:14 AM   #2
pmiguel
Senior Member
 
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,315
Default

You can find it here:

http://www.ensembl.org/info/data/ftp/index.html

--
Phillip
pmiguel is offline   Reply With Quote
Old 10-18-2012, 06:39 AM   #3
HSV-1
Member
 
Location: asia

Join Date: Jul 2012
Posts: 38
Default

the same is much bigger than the one from ucsc, why?
HSV-1 is offline   Reply With Quote
Old 10-19-2012, 06:32 AM   #4
mbblack
Senior Member
 
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245
Default

Quote:
Originally Posted by HSV-1 View Post
the same is much bigger than the one from ucsc, why?
How did you get your one from UCSC? If you make a RefGene based GTF from TableBrowser, it only includes coding features. The pre-built GTF from Ensembl includes all coding and non-coding features. Plus the actual annotations are longer text strings (all the Ensembl accessions for gene ID, exon ID, transcript ID, name, biotype,...) so in raw text the Ensembl file will be larger.

Also note that the UCSC file uses the notation "chr1", etc while the fist column in the Ensembl will just be "1" etc (some software will expect the prefix "chr").
__________________
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
mbblack is offline   Reply With Quote
Old 10-19-2012, 05:48 PM   #5
HSV-1
Member
 
Location: asia

Join Date: Jul 2012
Posts: 38
Default

This is probably the reason.
How to fix?
From the same sequence data with ensemble gft I should get more accepted hits by tophat .



Quote:
Originally Posted by mbblack View Post
How did you get your one from UCSC? If you make a RefGene based GTF from TableBrowser, it only includes coding features. The pre-built GTF from Ensembl includes all coding and non-coding features. Plus the actual annotations are longer text strings (all the Ensembl accessions for gene ID, exon ID, transcript ID, name, biotype,...) so in raw text the Ensembl file will be larger.

Also note that the UCSC file uses the notation "chr1", etc while the fist column in the Ensembl will just be "1" etc (some software will expect the prefix "chr").
HSV-1 is offline   Reply With Quote
Old 10-22-2012, 06:17 AM   #6
mbblack
Senior Member
 
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245
Default

Quote:
Originally Posted by HSV-1 View Post
From the same sequence data with ensemble gft I should get more accepted hits by tophat .
No, not for a reasonably mature genome such as the Rat. Ensembl's build may include a handful of novel and/or predicted coding genes, but not many. Ensembl Rat rel. 66.34 had 22,938 coding genes, 22,921 of which were known and have Refseq annotation (I only know this as I'm writing up data that used 66.34 as the reference - you would have to look on Ensembl's web site for the stats for the current release).

The annotation really should not have any significant affect on your summarized mapping results for a mature feature set like the Rat - it would only matter if there were a large number of novel, unknown or predicted genes in one annotation versus another, or if the splice boundaries of the annotation features were still largely undetermined. But once summarized by gene, your mapped count data should be unaffected given the genome build is fairly well characterized and stable at this point.
__________________
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
mbblack is offline   Reply With Quote
Reply

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 07:02 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO