[mira_talk] Re: Help with MCVc (missing Co Verage in consenus) after mapping assembly
- From: Austen Chen <cyausten@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 17 Feb 2014 14:57:55 +1030
Hi All,
Just let you know that i have tried all your suggestions by converting the
files to sam but failed to generate bam files for some reason; however I
have instead used convert_project to generate all the files (such as
featureanalysis.txt and featuresequences.txt) from which i was able to find
all SNPs and missing regions in my strains comparing to the reference,
which was great. Also i want to know if the reference has regions that are
missing but not in my strains and i seem to unable to find this piece of
information (after comparing 6 strains to the same reference). just want to
clarify it with you that if the files especially the feauturesequences.txt
do provide this kind of information and simply because all my strains do
not have extra regions than the reference and that's why they aren't shown
up?
Any help? and thank you very much
Austen
On Wed, Feb 5, 2014 at 6:04 AM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On 04 Feb 2014, at 14:22 , Austen Chen <cyausten@xxxxxxxxx> wrote:
>
> [...]
> Presumably A1 and A3 would have a common missing region from
> 165410-165814, but this is not the case as each missing position in A1 and
> A3 is not referring to the same position in relation to the reference
> sequence, and hope i have explained it here clearly. it looks like i am
> able to find missing coverage in each strain but unable to find common
> missing coverage between these 2 strains, and that's why I was asking you
> for help if my interpretation was correct and you could give me some
> suggestions on how to tackle this problem.
>
>
> As I wrote: convert the gap4 database (with your edits) back to CAF, then
> use "miraconvert -t cstats" to recreate some standard info files of MIRA,
> but using that new CAF file. You should get a new info file about consensus
> tags, which contains also the MCVc tags, have a look at that file. Though
> I'm not sure whether these positions would be really wrt to the reference,
> I need to check.
>
> Anyway, converting to SAM *should" give you positions which are based on
> the reference (there is no other way), you'd just need to parse out the
> tags out of the SAM.
>
> HTH,
> B.
>
>
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