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  • 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, 10:53 AM.

  • #2
    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

    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
    Last edited by svl; 09-16-2010, 02:16 PM.

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