My output of BWA index has only 4 files as
I read a thread that a guy's BWA index output has 8 different output data as
Does my bwa index wrong with some problem because when I do BWA aln with reads, there is no .sai oupput anyway?
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
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:
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 :)
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.
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
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?
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?
I would suggest to use the same version to index and then align.
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