[mira_talk] Re: Paired end info - SAM/BAM output from MIRA?
- From: "Raj Kumar, Praveen Kumar Mr." <rajkump@xxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 30 Sep 2010 21:26:09 -0400
Hi,
I am trying to output my mapping assembly in MAF format with this option
(-OUT:orc=yes:ora=no:ota=no:otc=no:otm=yes).......but ended up in the following
========================= Parameter parsing error(s) ==========================
* Parameter section: '-OUT'
* unrecognised string or unexpected character: otm
* Parameter section: '-OUT'
* unrecognised string or unexpected character: yes
* (may be due to previous errors)
===============================================================================
Thank you,
________________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] On Behalf
Of Peter [peter@xxxxxxxxxxxxxxxxxxxxx]
Sent: Thursday, September 30, 2010 10:14 AM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Paired end info - SAM/BAM output from MIRA?
On Thu, Sep 30, 2010 at 2:46 PM, Daniel Depledge <d.depledge@xxxxxxxxx> wrote:
>
> Hi Peter,
>
> I have now had a chance to run your script against a MIRA reference
> assembly of a paired-end solexa run for H1N1 flu. I had no troubles with
> the updated script and the sam output was then run through a number of
> samtools packages (and other scripts i have available) to ensure that full
> functionality was retained (it was).
>
> I have also checked the script against some single and paired-end 454 data
> and everything works very nicely.
>
> Regards
>
> Dan
Hi all,
My thanks to Dan for his testing. I have attached the current version
for wider trial, use at your own risk etc.
There is plenty of scope for improvement:
MIRA3 puts a lot of stuff into RT lines (read tags). These might
be stored in the SAM/BAM read tags...
There are lots of things that could be added, like using the MAF
ST and/or MT lines to record the sequencing type via the RG
(read group) and PL (platform) tags. Perhaps also the SN lines
(strain information) could be done with a SAM read group?
Perhaps I should look at MIRA's AO lines (as well as the AT
line) when constructing a CIGAR string?
Note this is a Python script, and currently uses Biopython. That
dependency could be avoided with a little more effort if there
was demand for this (e.g. to include it with MIRA).
Peter
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