Bwa Indexing

Question

[Kssr]

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.

[lh3]

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

[Houkto]

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.

[Houkto]

check http://seqanswers.com/forums/showthread.php?t=9808 this link for an answer.

[Leila.javanparast]

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?

[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.

[Leila.javanparast]

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

Answer 1

[Matt Shirley]

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.