[mira_talk] Re: Question: padded or unpadded outputs
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 19 Mar 2015 13:39:46 +0000
On Thu, Mar 19, 2015 at 1:25 PM, lenis vasilis <val1@xxxxxxxxxx> wrote:
> Hello Peter,
>
> I would like to ask you and something else that I noticed.
> I converted the maf out into sam and the sam into bam by using
> your maf2sam.py script as I said.
OK.
> I tried to convert this bam file into fastq and I noticed that includes
> reads only from one strand.
How did you do this (and why)?
> In order to construct this consensus I have used paired and reads,
> but as it seems Mira mapped only the reads from the first strand.
> Why is that?
MIRA might be fine. The problem could be in my script converting
from MIRA's *.maf file to SAM format. Which version of MIRA 4
are you using exactly? Perhaps there has been a subtle change
to the output which my script is not handling properly.
Or it might just be you have misunderstood the way SAM/BAM
stores paired reads and strand information (via the FLAG field
which is one of the most confusing things in the SAM format)?
If you can identify an example read pair where you think there
is a problem, then share with us the reads from the MAF and
SAM files that would help.
If need be can you share the entire MIRA *.maf file with me
(privately), e.g. via DropBox?
> Could you check the manifest file that I'm sending you in order
> to be sure that I wrote it alright?
Your manifest appears to use "autopairing" but I suggest you
look at the (early part of the) MIRA logging information from the
assembly to confirm it recognised your input data as pairs.
Peter
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