Bowtie & Samtools Questions with SOLiD data

[earisme]

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

[svl]

...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

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

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