Can I export DNA sequences from IGV?

[X. Yin]

Dear all,

I'm new to bioinformatics and my PI gave me serveral very large .BAM files (~200GB each) to analyze. Those files are so large that I can only use IGV to open them. Can I export the whole (or partial) mapping as a DNA sequence in IGV (similar to the "view DNA" function in the UCSC Genome Browser)?

Thanks and best wishes,
Xing

[James Robinson]

Hi,

Sorry but I don't understand what you want to do.   Do you want to export the reference sequence?  No, you can't do that from IGV,  it's rather trivial to do that directly from the fasta file.   This has nothing to do with bam files,  unless I am misunderstanding your question.

Jim

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[Xing Yin]

Dear Jim,

I don't want to export the reference sequence but the "sample" sequence. It seems that all the smaller sequences in each track have been aligned and mapped to the references, and we can see the mutations and insertions to references sequence in the "coverage" row. Can I export a most probable sequence from the "coverage"?

Thanks very much and Best wishes,
Xing

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[James Robinson]

Perhaps this will be useful,  scroll down to the "consensus sequence" description:  http://software.broadinstitute.org/software/igv/PopupMenus

However,  I think you probably want to do this from a scriptable analysis tool,  not a viz tool like IGV.

On Mon, Oct 16, 2017 at 3:36 PM, Xing Yin <xiy...@gmail.com> wrote:

Dear Jim,

I don't want to export the reference sequence but the "sample" sequence. It seems that all the smaller sequences in each track have been aligned and mapped to the references, and we can see the mutations and insertions to references sequence in the "coverage" row. Can I export a most probable sequence from the "coverage"?

Thanks very much and Best wishes,
Xing

On 10/16/2017 03:19 PM, James Robinson wrote:

Hi,

Sorry but I don't understand what you want to do.   Do you want to export the reference sequence?  No, you can't do that from IGV,  it's rather trivial to do that directly from the fasta file.   This has nothing to do with bam files,  unless I am misunderstanding your question.

Jim

On Mon, Oct 16, 2017 at 11:16 AM, X. Yin <xiy...@gmail.com> wrote:

Dear all,

I'm new to bioinformatics and my PI gave me serveral very large .BAM files (~200GB each) to analyze. Those files are so large that I can only use IGV to open them. Can I export the whole (or partial) mapping as a DNA sequence in IGV (similar to the "view DNA" function in the UCSC Genome Browser)?

Thanks and best wishes,
Xing

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[Dario Strbenac]

You will want to use a command such as samtools mpileup for such a task.