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Bwa Indexing

I am trying to index a reference genome using bwa index.

bwa index -a bwtsw xxx.fasta

It runs without errors and generates the following files with extensions .amb,.ann,.bwt,.pac,.sa.

I have never really done indexing myself before using bwa.However, I remember indexing generates other files as well such as .rpac,.rbwt,.rpac,.rsa.What does r indicate here? What are the files generated usually when we index a reference genome ? Any help is appreciated.

alignment
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updated by Leila.javanparast • Leila.javanparast • written by Kssr Kssr

Hi there,

I cannot answer your question regarding what are these files are used for ? But I can tell that you have index your reference genome successfully.

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written by Houkto • Houkto

0.5.x generates .r files, but 0.6.x does not.

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written by lh3 lh3

hi to all.I have a problem during index reference file. it stops and doesn't continue after 2 hours. I should mention that I'm doing the whole process on VMware on my windows 10. does it matter?

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written by Leila.javanparast • Leila.javanparast

Probably a memory shortage. Do yourself a favor and get native Linux, maybe via an external disk. That will save you a lot of VM-induced troubles that might come up. How much memory do you have?

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written by ATpoint ATpoint

Memory (RAM) not disk space.

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written by ATpoint ATpoint

My memory is 8GB. I supposed you mean the disk which is related to Vm.

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written by Leila.javanparast • Leila.javanparast

No, with memory I meant memory. And how much of these 8GB are allocated to the VM? Probably like half of it? This would explain the memory shortage as bwa typically uses somewhat 8GB for index creation.

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written by ATpoint ATpoint

I removed the previous discussion. Bottom line was that you do not have enough memory (RAM). Consider getting more RAM or try to switch to a more powerful computer. In case the issue persists please open a new question here on Biostars instead of warming up old threads. Please make sure to check on RAM consumption before opening a new question.

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written by ATpoint ATpoint

ok. I can not use another computer. do u think using original Linux instead of VM, would fix my problem?

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written by Leila.javanparast • Leila.javanparast

1 answer

The .r* files are reverse sequence index, BW-transformed sequence, suffix-array index. I think it uses these for reads on the minus strand, but I'm not sure. See class pac_rev.

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written by Matt Shirley Matt Shirley

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