Exporting data from IGV

[Sigal Starinsky]

Hi,

I would like to export the reads number to excel for statistics.

How can I do that in IGV?

Thanks

[igv-help]

What do you mean by "reads number"?

[Sigal Starinsky]

I want to calculate the average of the reads of all the bases in the negative control samples, so I need a table of all the reads.

[igv-help]

That's not possible with IGV.

[Sigal Starinsky]

Can I see the total read only per a base, once I click it? 

There is no way to see all the total reads?

[James Robinson]

Hi,

You asked for "the average of the reads of all the bases".   I assume you mean counts of each base?   You can't export that from IGV, which is primarily a visualization tool.   You might be able to compute what you are after with igvtools https://software.broadinstitute.org/software/igv/igvtools_commandline.    For the output file use the ".wig" option to get ascii text,  that is be sure the output filename ends with ".wig".

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