Question: BWA aln - failed to locate the index
0
gravatar for m.wekking
10 months ago by
m.wekking10
m.wekking10 wrote:

So I have alot of paired-end sequence samples in the formate sample_x_fw.fastq and sample_x_rv.fastq and want to align these with the BWA sampe command

so I downloaded the hg19.fasta and ran:

bwa index -p bwa_hg19 -a bwtsw hg19.fa

this resulted in:

  • bwa_hg19.amb
  • bwa_hg19.ann
  • bwa_hg19.bwt
  • bwa_hg19.pac
  • bwa_hg19.sa

after this I tried to run:

bwa aln bwa_hg19.fa sample_1_fw.fastq > aln_sa1.sai

and I get the error:

[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln] fail to locate the index

Does anyone have any idea what goes wrong?

bwa alignment bioinformatics • 806 views
ADD COMMENTlink modified 10 months ago by Pierre Lindenbaum129k • written 10 months ago by m.wekking10
1

quick question : why bwa aln and not the more recent bwa mem ? Are your reads small ( < 50bp ? )

ADD REPLYlink written 10 months ago by Nicolas Rosewick9.0k
3
gravatar for ATpoint
10 months ago by
ATpoint36k
Germany
ATpoint36k wrote:

It is bwa aln bwa_hg19 sample_1_fw.fastq > aln_sa1.sai as the prefix you gave for indexing is bwa_hg19, not bwa_hg19.fa

ADD COMMENTlink modified 10 months ago • written 10 months ago by ATpoint36k

That's it! thank you very much!

ADD REPLYlink written 10 months ago by m.wekking10
2
gravatar for Pierre Lindenbaum
10 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

try

bwa aln bwa_hg19 sample_1_fw.fastq > aln_sa1.sai

or

bwa index -a bwtsw hg19.fa
bwa aln hg19.fa sample_1_fw.fastq > aln_sa1.sai
ADD COMMENTlink written 10 months ago by Pierre Lindenbaum129k

That's it! thank you very much!

ADD REPLYlink written 10 months ago by m.wekking10
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