Bwa Index Output And Bwa Aln Problem

Question

[Tonyzeng]

My output of BWA index has only 4 files as

mm10.fa.amb mm10.fa.ann mm10.fa.bwt mm10.fq.pac

I read a thread that a guy's BWA index output has 8 different output data as

.amb .ann .bwt .pac .rbwt .rpac .rsa .sa

Does my bwa index wrong with some problem because when I do BWA aln with reads, there is no .sai oupput anyway?

thanks

[Tonyzeng]

by the way I used followings commands

$ bwa index -a bwtsw mm10.fa produced mm10.fa.amb; mm10.fa.ann; mm10.fa.bwt; mm10.fq.pac

$ bwa aln mm10.fa R1.fastqsanger > R1.sai produced 0 output R1.sai

Answer 1

[Charles Warden]

Looks like the correct command. Maybe there is something wrong with your mm10.fa file.

Either way, have you considered just downloading the pre-formatted reference? mm10 is a popular reference and Illumina provides indexed references for most programs:

http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn

[Tonyzeng]

Thanks a lot, cwarden. I can see that you have much experience on sequence analysis.

I performed BWA index by downloading pre-formatted reference from UCSC by concatenating all chromosomes from chromFa.tar.gz using command $ cat chr*.fa > mm10.fa.

But I will download indexed mm10 from linker you suggested and run BWA aln to see if it works or not.

Thanks again :)

Answer 2

[Ashutosh Pandey]

I am not sure but may be this can help you Do different versions of BWA create differently named index files?

I will go with the latest BWA.

[Ashutosh Pandey]

Did you put all the index files in one folder and then mention the path to it in your "bwa aln" command. It should be sth like

bwa aln Path_to_the_folder_containing_all_the_indexes\mm10.fa R1.fastqsanger > R1.sai

Try this.

[Tonyzeng]

Ashutoshmits, I run the bwa aln right under the folder that stores all the index files, so it should be not a problem. I also run with BWA-0.7.5a, a latest version of aligner.

Since I did BWA alignment by connecting to my lab master server that allocates my account with memory start with 2GB memory up to 6GB, 4 virtual processors and 100GB~HD. My computer runs so slow and I think that it is not power enough to run my data because of poor computer capacity. Maybe this is the reason it failed?

[Tonyzeng]

Seems like the index reference files produced in the linker are based on BWA 0.5 or 0.6 (http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn). It is not a good idea to use these index file for alignment since I am using BWA 0.7.5a, right?

[Ashutosh Pandey]

I would suggest to use the same version to index and then align.