Question: Burrows Wheeler Aligner - tool
0
gravatar for sruthi
10 months ago by
sruthi20
sruthi20 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 • 335 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 10 months ago by sruthi20

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

ADD REPLYlink written 10 months ago by h.mon29k

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 9 months ago by sruthi20

What is the reason that you chose bwtsw ?

ADD REPLYlink written 10 months ago by lakhujanivijay4.7k

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

ADD REPLYlink written 9 months ago by sruthi20
0
gravatar for Joe
10 months ago by
Joe16k
United Kingdom
Joe16k wrote:

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

bwa Version: 0.7.17-r1188

ADD COMMENTlink written 10 months ago by Joe16k

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

ADD REPLYlink written 9 months ago by sruthi20
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