SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Error Bowtie with fastq files (from Solid .csfasta & .qual) pepperoni Bioinformatics 0 10-12-2011 08:20 PM
questions about samtools mpileup & bcftools chenjy Bioinformatics 0 07-26-2011 04:21 AM
BWA align SOLiD PE data gives poor mapping & 0.5% properly paired alig Bioinformatics 3 07-08-2011 08:44 AM
[B]Bowtie and Samtools questions[/B] dicty Bioinformatics 3 12-07-2010 12:15 PM
Bowtie and samtools questions dicty Bioinformatics 0 12-01-2010 12:51 PM

Reply
 
Thread Tools
Old 09-16-2010, 10:44 AM   #1
earisme
Junior Member
 
Location: Sacramento

Join Date: Jun 2010
Posts: 1
Default Bowtie & Samtools Questions with SOLiD data

Hi there,

I just started learning bioinformatics and am working at aligning SOLiD (colorspace) sequence reads in order to find SNPs. I used Bowtie and Samtools to build and align the reads to a reference genome (which I converted to colorspace) but I am going crazy scrolling through the window of samtools tview and manually recording SNPs - I have spent 2 days doing this and I am not even 1/10000 of the way through.

I know that there has to be an easier way to visualize the SNPs (i.e. I would like a csv file that I can open in excel that shows all SNPs), does anyone know how to do this?

Also, when I visualize the alignment in tview all I have is a consensus sequence, it does not show me the reference genome sequence. Does anyone know how to have the reference genome display on the top. All I am seeing is N's.

[I am using Putty as a terminal to access an Amazon Web EC2 computer. My files are Linux-based.]

Please help!

Thanks,
Beth

Last edited by earisme; 09-16-2010 at 10:53 AM.
earisme is offline   Reply With Quote
Old 09-16-2010, 01:34 PM   #2
svl
Member
 
Location: Netherlands

Join Date: Sep 2009
Posts: 43
Default

Quote:
Originally Posted by earisme View Post
...but I am going crazy scrolling through the window of samtools tview and manually recording SNPs. I know that there has to be an easier way to visualize the SNPs
Thanks god yes

Quote:
I would like a csv file that I can open in excel that shows all SNPs
Since you're already using SAMTOOLS, have a look at the pileup command/format: http://samtools.sourceforge.net/pileup.shtml One of the columns shows whether the reads overlapping a single nucleotide (on the reference) agree with the reference or not, you can use this to extract the ones where many (say 20% or more) do not agree with the reference (= a possible single nucleotide variant or polymorphism).

Also have a look at the SNP_discovery software hub on the wiki: http://seqanswers.com/wiki/Special:B...=SNP_discovery

Crossbow for instance, combines bowtie with soapsnp: http://seqanswers.com/wiki/Crossbow

Quote:
Also, when I visualize the alignment in tview all I have is a consensus sequence, it does not show me the reference genome sequence.
For visualizing alignments (in eg SAM or BAM format) I recommend you to have a look at IGV: http://www.broadinstitute.org/igv/ I find it very useful.

For an overview of viewers: http://lh3lh3.users.sourceforge.net/NGSalnview.shtml

Last edited by svl; 09-16-2010 at 02:16 PM.
svl 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 05:24 PM.


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