Question: Bwa Index Output And Bwa Aln Problem
1
gravatar for Tonyzeng
5.2 years ago by
Tonyzeng300
Tonyzeng300 wrote:

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

bwa • 11k views
ADD COMMENTlink modified 5.2 years ago by Ashutosh Pandey11k • written 5.2 years ago by Tonyzeng300

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

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Tonyzeng300
0
gravatar for Charles Warden
5.2 years ago by
Charles Warden5.8k
Duarte, CA
Charles Warden5.8k wrote:

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

ADD COMMENTlink written 5.2 years ago by Charles Warden5.8k

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 :)

ADD REPLYlink written 5.2 years ago by Tonyzeng300
0
gravatar for Ashutosh Pandey
5.2 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

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.

ADD COMMENTlink written 5.2 years ago by Ashutosh Pandey11k

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.

ADD REPLYlink written 5.2 years ago by Ashutosh Pandey11k

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?

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Tonyzeng300

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?

ADD REPLYlink written 5.2 years ago by Tonyzeng300

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

ADD REPLYlink written 5.2 years ago by Ashutosh Pandey11k
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