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Loading many files with a batch script

asked 2015-04-05 14:34:51 -0600

Olga Botvinnik gravatar image

I have hundreds of bam files I would like to view using GenomeBrowse. In IGV, I can write a batch script which will load many bam files at once. Is this possible in GenomeBrowse?

It seems that as a stop-gap measure, one could write a regular IGV batch script, save the session, and import the IGV session into GenomeBrowse.

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answered 2015-04-27 09:22:07 -0600

Hi Olga,

GenomeBrowse does not currently have batch script capabilities directly, so the only way to load a large number of files automatically is through the process of using the IGV functionality as you have described.

GenomeBrowse does have that ability to drag and drop files into the plotting window. So another option would be to open a file explorer to the location of all of your BAM files and then drag and drop the ones you would like to visualize directly into the plot window.

Depending on the size of the files you may want to use our command line program "gautil" to first compute index and coverage for the files so these computation does not overwhelm your system. See our manual for further details.

Let me know if you have any further questions.

Thanks, Jami...

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Asked: 2015-04-05 14:34:51 -0600

Seen: 89 times

Last updated: Apr 27 '15