SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SNP function prediction in non-human species spark Bioinformatics 7 01-22-2013 01:45 AM
Creating custom reference genome from BED files? ngseq Illumina/Solexa 0 09-27-2012 09:10 AM
Does GATK only work for human species? AllenLee_china Bioinformatics 4 06-25-2012 01:44 AM
1000 genome data and other human ref sequence differ johnadam33 Bioinformatics 4 01-05-2011 02:16 AM
creating Roche's sff files enna80 Bioinformatics 5 11-10-2010 05:30 AM

Reply
 
Thread Tools
Old 11-28-2012, 12:23 AM   #1
Stina
Junior Member
 
Location: Norway

Join Date: Feb 2012
Posts: 9
Default Which .fa files should I include when creating a ref. genome of a non-human species?

I intend to analyse HTS resequencing data from a capture experiment in dogs and I am trying to create a reference genome to use for the analysis. I want to use the FASTA files at ensemble. The FASTA files available here are from: chr 1-38, MT, X and nonchromosomal, but none for the Y chromosome... Should I include the MT and nonchromosomal data when creating a reference genome file? And if so, where should I place them (in what order)?

Many thanks in advance!
Stina is offline   Reply With Quote
Old 11-28-2012, 04:01 AM   #2
mbblack
Senior Member
 
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245
Default

When mapping my RNA-seq data, I make two files. One is the reference genome I am mapping to, the other is a filter reference file for reads to be excluded from mapping (mtDNA, rRNA and all non-coding sequences). Most mapping tools will let you use such a filter reference to exclude reads and thus not waste time and compute resources mapping them to the full reference genome.
__________________
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
mbblack is offline   Reply With Quote
Old 11-28-2012, 06:20 AM   #3
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

mbblack has a good suggestion. As to your exact question of "...where should I place them..." it matters not. I suspect that most people put them after the numbered chromosomes.
westerman is offline   Reply With Quote
Old 11-28-2012, 11:50 PM   #4
Stina
Junior Member
 
Location: Norway

Join Date: Feb 2012
Posts: 9
Default

Thanks for the advice!
Stina 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 07:18 PM.


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