Open files created with bwa

Question

[mostafarafiepour]

Hi All,

I indexed the human reference genome using bwa software (bwa index option) And the following files were created for me:

GCF_000001405.39_GRCh38.p13_genomic.fna.bwt
GCF_000001405.39_GRCh38.p13_genomic.fna.pac
GCF_000001405.39_GRCh38.p13_genomic.fna.amb
GCF_000001405.39_GRCh38.p13_genomic.fna.ann
GCF_000001405.39_GRCh38.p13_genomic.fna.sa
GCF_000001405.39_GRCh38.p13_genomic.dict
GCF_000001405.39_GRCh38.p13_genomic.fna.fai

So, I used head -n 10 to open them, but I got an error and the files do not open for me with this option? In my online search, I could not find a solution to open them !!

What is the best idea?

[Kevin Blighe]

These are index files - why do you need to open them? Please show the exact commands that you have been using, and also show the output of:

pwd
ls -l

[mostafarafiepour]

I want to see what structurally indexed files are different from genome references?

[Ram]

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image or the HTML embed code, not the link to the webpage that has the image embedded (which is what you have used here)

[Kevin Blighe]

I mean, if you are in the same directory, they should open no problem. Take a look:

head -100000 hg38.fasta > small.fasta

bwa index small.fasta small
[bwa_index] Pack FASTA... 0.13 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 3.22 seconds elapse.
[bwa_index] Update BWT... 0.07 sec
[bwa_index] Pack forward-only FASTA... 0.07 sec
[bwa_index] Construct SA from BWT and Occ... 1.56 sec
[main] Version: 0.7.17-r1188
[main] CMD: /Programs/bwa-0.7.17/bwa index small.fasta small
[main] Real time: 5.887 sec; CPU: 5.052 sec

ls -l
total 7437244
-rw-rw-r-- 1 kblighe kblighe 1020663364 Jun 25 20:24 hg38.1.bt2
-rw-rw-r-- 1 kblighe kblighe  762328952 Jun 25 20:24 hg38.2.bt2
-rw-rw-r-- 1 kblighe kblighe      15065 Jun 25 16:18 hg38.3.bt2
-rw-rw-r-- 1 kblighe kblighe  762328946 Jun 25 16:18 hg38.4.bt2
-rw-rw-r-- 1 kblighe kblighe 3273481150 Sep 28  2017 hg38.fasta
-rw-rw-r-- 1 kblighe kblighe      19381 Jul 25 09:35 hg38.fasta.fai
-rw-rw-r-- 1 kblighe kblighe 1020663364 Jun 26 00:07 hg38.rev.1.bt2
-rw-rw-r-- 1 kblighe kblighe  762328952 Jun 26 00:07 hg38.rev.2.bt2
-rw-rw-r-- 1 kblighe kblighe    5099955 Nov 23 08:41 small.fasta
-rw-rw-r-- 1 kblighe kblighe         83 Nov 23 08:41 small.fasta.amb
-rw-rw-r-- 1 kblighe kblighe         39 Nov 23 08:41 small.fasta.ann
-rw-rw-r-- 1 kblighe kblighe    5000048 Nov 23 08:41 small.fasta.bwt
-rw-rw-r-- 1 kblighe kblighe    1249989 Nov 23 08:41 small.fasta.pac
-rw-rw-r-- 1 kblighe kblighe    2500024 Nov 23 08:41 small.fasta.sa

head small.fasta.ann
4999950 1 11
0 chr1 (null)
0 4999950 5

head small.fasta.amb 
4999950 1 5
0 10000 N
207666 50000 N
297968 50000 N
535988 50000 N
2702781 43509 N

The other index files (bwt, pac, sa) are binary, I think.

[mostafarafiepour]

Exactly these three files (bwt, pac, sa) will not open.

[Kevin Blighe]

They do open but they are in binary format.

[WouterDeCoster]

Not all files contain information that has a meaningful text representation for humans.

[mostafarafiepour]

I asked you to provide a solution to open these files, not to comment on the contents.

[WouterDeCoster]

And I told you you can't open the files in any meaningful way, so there is no solution.

[Ram]

Please do not be rude - ordering people around is unprofessional.