Building an index using xenome
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5 weeks ago
salehm • 0

Hi,

I am using xenome to distinguish between reads map to human genome from those maps to mouse genome in RNA seq data from patient derived xenografts (PDX). I am trying to build an index using "xenome index" for mouse and human primary assemblies. But it always gives an error: "could not find the human genome assembly". Please see the screenshot attached. Error message Is there a way I could get around it?

Thanks.

PDX • 154 views
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The file is not present at this location. What is the output of ls in that folder?

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Thanks ATpoint for your response. both human and mouse genome files together with the software container image are all in the this directory. I also tried binding this directory to the container but still not able to find the files. please see the screen shot. enter image description here

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