SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
need GRCh37 database moty Bioinformatics 13 03-23-2012 03:37 PM
Homo_sapiens. GRCh37.55.gtf for tophat shouguogao RNA Sequencing 2 12-16-2011 02:51 AM
Eland - GRCh37/hg19 assembly AnotherHTS Bioinformatics 2 10-21-2010 07:27 AM
how to match snp position to GRCh37 release? cheng Bioinformatics 1 10-06-2010 03:12 PM
RepeatMasker report of GRCh37 alanwan General 0 08-23-2010 05:46 PM

Reply
 
Thread Tools
Old 07-13-2012, 01:09 AM   #1
yujiro
Junior Member
 
Location: tokyo

Join Date: Jul 2010
Posts: 5
Default GRCh37: how to use latest patches?

I would like to know how to assemble human refefence genome GRCh37 from individual chromosome files and latest patches.

This is ensembl's ftp site which lists >300 fasta files.
ftp://ftp.ensembl.org/pub/release-67...o_sapiens/dna/

For primary assembly, one might simply concatenate chromosome 1, 2, ..., X, and Y. However, X and Y chromosomes share pseudoautosomal region (PAR) as README points out. I could just leave out Y chromosome since I work on K562 cells, but otherwise what am I supposed to do? There is a big file called toplevel.fa which appears to have PAR sequenes masked, but does it contain all chromosomes and patches? README does not say anything about its content.

There seem to be two kinds of patches: fixes and novel additions. How are these patches correctly incorporated into the primary assembly? Is there a utility software to handle this? Or are patches treated as separate entities (e.g. as PATCH_xxx instead of being integrated into chromosome proper)?

Thank you for your very kind help.

Last edited by yujiro; 07-13-2012 at 03:20 AM.
yujiro is offline   Reply With Quote
Reply

Tags
assembly, ensembl, patches, reference genome

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 05:24 PM.


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