Question: Burrows Wheeler Aligner - tool
0
gravatar for sruthi
22 months ago by
sruthi30
sruthi30 wrote:

Hi, I'm new to BWA tool. I indexed my reference.fa using command:

bwa index -a bwtsw reference.fa reference_prefix

and got 3 output files: .amb .ann .pac

I read that the above command must produce 8 output files such as .amb .ann .bwt .pac .rbwt .rpac .rsa .sa.

As only 3 output files have been generated, has the command run successfully? If not what should I do?

TIA

sequencing alignment • 567 views
ADD COMMENTlink modified 21 months ago by Biostar ♦♦ 20 • written 22 months ago by sruthi30

bwa index output some messages to the screen, what did they say?

ADD REPLYlink written 22 months ago by h.mon32k

Hey, So the messages displayed are: 1. bwa_index Pack FASTA 2. Construct BWT for the packed sequence 3. BWT_gen 4. Update BWT 5. Pack forward only FASTA 6. Construct SA from BWT and Occ...

ADD REPLYlink written 22 months ago by sruthi30

What is the reason that you chose bwtsw ?

ADD REPLYlink written 22 months ago by lakhujanivijay5.4k

Hey, I chose bwtsw as the genome I'm analysing is of larger size, say 3.3 GB. Hence.

ADD REPLYlink written 22 months ago by sruthi30
0
gravatar for Joe
22 months ago by
Joe18k
United Kingdom
Joe18k wrote:

That command produces 5 files for me: .amb, .ann, .bwt, .pac and .sa.

bwa Version: 0.7.17-r1188

ADD COMMENTlink written 22 months ago by Joe18k

Hey healey, I ran the command for the second time and got all these 5 files as the output. Thanks.

ADD REPLYlink written 22 months ago by sruthi30
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