[mira_talk] Re: Solexa paired-end reads
- From: Louis Letourneau <louis.letourneau@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 23 Feb 2011 12:21:20 -0500
I might be completely off here, since I haven't tried the procedure
myself, but PICARD has a command to fix ISize information from bam files
if this is the only thing that is missing to bring tablet happiness.
http://picard.sourceforge.net/command-line-overview.shtml#FixMateInformation
or it might just be that mates aren't represented as such in the bam
(columns 7,8 +bit field. Fix mate will fix column 9)
Louis
On 11-02-23 12:13 PM, Tony Travis wrote:
> On 23/02/11 16:59, Peter wrote:
>> [...]
>> I don't really expect them to when there are more well defined file
>> formats out there. Consider that MIRA already supports at least 3
>> different pair-end naming conventions, so for Tablet to try and
>> guess what's in the ACE file is quite tricky.
>
> Hi, Peter.
>
> I use the MIRA ace file because I'm still using Consed, but I now want
> to get a better overview of my 454 + Solexa assembly using Tablet.
>
>> I'm hoping that if there is enough demand, the Tablet team might
>> be persuaded to support the MIRA assembly format (MAF) directly.
>> This does have explicit pair information (although not as helpful as
>> SAM/BAM in that you have to scan the whole file to find the mate
>> pairs). Plus the MAF (and ACE) files can contain contig region tag
>> information which SAM/BAM does not support.
>
> I had to do quite a lot of work to get a sorted and indexed BAM file
> from the SAM file your Python script created. After all that, Tablet
> told me that the "samtools" installed in Bio-Linux6 is too old :-)
>
> It loaded it, though...
>
>> [...]
>>>> I'm happy to have any feedback on the MIRA list.
>>>
>>> OK, brace yourself ;-)
>
> Your script was useful, but unless I'm doing something wrong with it
> quite a bit of post-processing is needed to get a BAM file that Tablet
> can use to display mate-pairs, and all insert sizes are reported as zero...
>
> Maybe I'll go back to trusty old Hawkeye ;-)
>
> Thanks again for the jungle tip,
>
> Tony.
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
