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
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
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