[mira_talk] Re: Question: padded or unpadded outputs
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 18 Mar 2015 09:38:02 +0000
On Tue, Mar 17, 2015 at 9:38 PM, lenis vasilis <val1@xxxxxxxxxx> wrote:
> Thank you very much for your support.
> I'm really sorry for annoying you again but I'm a little bit confused.
> As I understand (and I'm not so sure about that) the unpadded file
>
is the consensus after the corrections that Mira did into the previous run.
> I tried to visualize it on igv by converting the maf file into bam.
>
The key point here is MIRA's SAM/BAM output is for use with
MIRA's padded FASTA file.
If you want to view a SAM/BAM file with the unpadded FASTA file,
you first need to run "samtools depad" on the MIRA SAM/BAM file
to make an unpadded BAM file:
$ samtools depad -S -u -T mira_padded.fasta mira_padded.sam >
mira_unpadded_unsorted.bam
Then sort and index the BAM file as usual.
See also my blog post (from before padded/unpadded references
were officially included in the SAM/BAM file format v1.5), which has
screenshots from both IGV and Tablet showing insertions using
a padded or unpadded reference:
http://blastedbio.blogspot.co.uk/2011/09/sambam-with-gapped-reference.html
I prefer Tablet for these viewing SAM/BAM files with a padded reference
because it handles both gapped and ungapped coordinates nicely.
Tablet will also handle the ACE output from MIRA, which also
shows the padded reference nicely.
Peter
Other related posts:
