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Indexing Genome Commands in Linux (hummingbird-ucsc)

Hey all,

I am having trouble indexing my reference genome (mm10) with bowtie 2. It keeps stalling / lagging after it starts indexing. As in it begins, but then gets stuck in a loop soon after and cannot finish. Anyone else run into this problem? Or know another way to go through indexing a genome for Chip-Seq?

chip-seq linux bowtie2
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updated by Biostar Biostar • written by Scott McKay • Scott McKay

You may not have enough RAM (how much do you have ?). Use htop or free -g to find out.

If you don't have enough, the mapping step might also not work.

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written by colindaven colindaven

Hello Scott McKay!

We believe that this post does not fit the main topic of this site.

OP did not follow up.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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