SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Genome Res De novo bacterial genome sequencing: millions of very short reads assembly b_seite Literature Watch 1 10-04-2017 11:26 PM
How to map 454 reads/contigs to a mitochondrial genome? fruktimport Bioinformatics 2 03-28-2011 10:35 AM
Short reads fragments of genome... hicham Bioinformatics 2 03-24-2010 04:15 AM
looking for reference genome based assembler for short-reads zchou Bioinformatics 3 12-16-2009 08:13 PM
Haman genome alignment with short reads ptongyoo Bioinformatics 4 04-14-2009 05:27 PM

Reply
 
Thread Tools
Old 08-02-2011, 07:11 AM   #1
ynwh
Member
 
Location: MD

Join Date: Jul 2011
Posts: 16
Default How to map short reads to a distant genome?

Hi,

My current project involves mapping short reads to the reference genome from another species (reads and reference genome belong to the same genus), e.g. mapping chimp reads to human genome. I want to know if this type of mapping is possible and if it is possible, Do the results has any meaning?

In other words, I want to know whether current short reads mapping algorithms (BWA, MAQ etc.) can give useful results when deal with somewhat distant genomes (same genus but different species)?

Many thanks

--Hao
ynwh is offline   Reply With Quote
Old 08-02-2011, 12:08 PM   #2
GW_OK
Senior Member
 
Location: Oklahoma

Join Date: Sep 2009
Posts: 411
Default

I wouldn't call chimp and human that distant. I was once given some chimp labeled as human in a comedy of errors and it aligned just fine (using BWA). I thought I had found some REALLY rare mutations before the problem became obviously apparent, lol.

How are you defining useful and meaningful? Are you just wanting a scaffold to do some de novo assembly? This should work for that...
GW_OK is offline   Reply With Quote
Old 08-02-2011, 12:22 PM   #3
ynwh
Member
 
Location: MD

Join Date: Jul 2011
Posts: 16
Default

Hi GW_OK,

Many thanks for your response. "Useful and meaningful" means when I find some PAV, CNV or mutations between two species, these findings are real and not artifacts of algorithm.

If chimp and human are not far enough, what do you think if I map two plants, e.g. wild rice to domesticated rice (O. sativa). Plant genomes are more dynamic then animals because of TEs
ynwh is offline   Reply With Quote
Old 08-02-2011, 01:11 PM   #4
GW_OK
Senior Member
 
Location: Oklahoma

Join Date: Sep 2009
Posts: 411
Default

I would not use any CNV/SNP/Indel/mutation based on anything other than alignment of one species against itself. How could you tell if it was an alignment artifact or there really are differences between the species.

A disparate species alignment is really only good for de novo scaffolding, as far as I know (anyone else can feel free to correct me).


Edit: Or are you attempting to use this assembly as some sort of round-about BLAST?
GW_OK is offline   Reply With Quote
Old 08-02-2011, 04:41 PM   #5
ynwh
Member
 
Location: MD

Join Date: Jul 2011
Posts: 16
Default

Yeah. What I want to do is to blast short reads against the reference genome. But the reads number are too high to do a BLAST search. Do you have any recommendation on what program can do such job?
ynwh is offline   Reply With Quote
Old 08-03-2011, 05:56 AM   #6
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838
Default

Quote:
Yeah. What I want to do is to blast short reads against the reference genome. But the reads number are too high to do a BLAST search. Do you have any recommendation on what program can do such job?
Bowtie is fairly fast at its job, and is able to handle up to 3 SNPs in the seed (by default 29bp), but setting it for that low stringency will make it take much longer and produce more false positive hits.
gringer 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 04:39 PM.


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