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skingan · 07-29-2010, 01:02 PM

Hi,

We are using IMAGE to fill in gaps of our genome assembly but are not sure how to generate the required input files:

contigs.fa.original and
read.placed.original
(http://sourceforge.net/apps/mediawik...w_to_run_IMAGE)

Our initial assembly is done with BWA. Does anyone have a script that can use a BAM file (the BWA output) to generate contigs.fa.original and read.placed.original?

Thanks!

Sarah Kingan

07-29-2010, 01:02 PM	#1
skingan Member Location: San Mateo, CA Join Date: Feb 2010 Posts: 17	IMAGE input files Hi, We are using IMAGE to fill in gaps of our genome assembly but are not sure how to generate the required input files: contigs.fa.original and read.placed.original (http://sourceforge.net/apps/mediawik...w_to_run_IMAGE) Our initial assembly is done with BWA. Does anyone have a script that can use a BAM file (the BWA output) to generate contigs.fa.original and read.placed.original? Thanks! Sarah Kingan