Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Human Reference Genome Mucki0815 General 9 01-10-2013 12:08 PM
how to retrieve human rRNA annotation Xi Wang RNA Sequencing 11 03-26-2012 12:11 AM
Cuffcompare reference annotation gokhulkrishnakilaru Bioinformatics 0 02-23-2012 07:43 AM
General mapping rate of human resequencing data against reference in GAiix/Hiseq cybog337 Illumina/Solexa 2 01-12-2011 09:43 AM
Why do we use mapping programs instead of blast for mapping to a reference? thsuk1 Bioinformatics 6 08-27-2010 09:54 AM

Thread Tools
Old 04-23-2012, 01:17 AM   #1
Location: Sydney, Australia

Join Date: Jan 2012
Posts: 61
Question Reference annotation for mapping (human)?

Which annotation is best for reference-based/guided mapping and assembly using Tophat/Cufflinks/other tools?

UCSC Comprehensive Gencode11 track, downloaded as a .gtf, has 2072303 records.

ENSEMBL66 [Homo_sapiens.GRCh37.66.gtf] has 2181086 records.

gencode11 (on which ENSEMBL is based(???)) has 2617472 records, of which:
1947538 gencode.v11.annotation.level_1_2.gtf
586834 gencode.v11.annotation.level_3.gtf
74062 gencode.v11.polyAs.gtf
9038 gencode.v11.2wayconspseudos.gtf

Or, what are the pros/cons of using each of them? And what is the actual difference?

Thanks in advance!
dvanic is offline   Reply With Quote
Old 04-24-2012, 07:56 PM   #2
Location: Sydney, Australia

Join Date: Jan 2012
Posts: 61

*bumping up my own post, since this is still relevant*
(Thanks in advance!)
dvanic 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 02:09 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO