creating .genome files via command line

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kevi...@stanford.edu

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Sep 30, 2017, 5:07:09 AM9/30/17
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Dear IGV team,

I would like to create .genome files for hundreds of different .fasta files, and wanted to know if there is a way to do this via command line.  I could not find such a command associated with the igvtools package.  

In case you're wondering why I would want so many different .genome files, the purpose of this is to look at alignments for sequencing data on many different plasmids.

Thanks in advance,

Kevin

James Robinson

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Sep 30, 2017, 12:56:27 PM9/30/17
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Hi,

There is no function to do this, but neither is it necessary.    Index your fasta files with either samtools (faidx) or igv tools,  then use the fasta files as a reference.   ".genome" files are only needed to create sharable files that load both reference (fasta) and annotations together,  they are never required as you can always load the two indpendently.

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