[mira_talk] Re: Help with MCVc (missing Co Verage in consenus) after mapping assembly
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 4 Feb 2014 09:23:04 -0500
On Feb 4, 2014, at 8:22 AM, Austen Chen <cyausten@xxxxxxxxx> wrote:
> Firstly I apologise for invading your privacy which was done unintentionally.
> After sending the email I couldn't see it on the list, so i wasn't sure if
> it's being sent or not, and with your name and photos popping out everywhere
> on the web page, looks like you were happy for people to contact you and
> that's why i thought i could just ask you if i had sent my mail successfully,
> and i didn't mean to demand a response from you straightaway, and i know you
> are very helpful and quick in response, and there is no need to do so, so
> merely misunderstanding and sorry to have upset you.
>
> Still thank you very much for your help, and i don't think I had explained my
> problem clearly. you are right that I made a mapping, imported that into
> gap4, made some edits/finishing there and then exported the tag positions
> from within gap4. this tag position has been illustrated in your mira manual
> page 17 (version 4.0rc5): Figure 1.18 "MCVc" tag showing a genome deletion
> in Solexa mapping assembly. as you can see in the figure the top line is a
> bacterial reference sequence, and the missing dark red stretch in the
> consensus is given at a position of 554830 in reference to the reference
> sequence. what i have done is that i have made two separate mapping
> assemblies, one is A1 against an annotated GenBank bacterial reference
> sequence, and another is A3 against the same reference sequence, and I want
> to find if A1 and A3 have any common missing regions, and that's where i had
> my problem. For example, as you can see in Gap4 A1 has no coverage at a
> position of 165410 with a missing length of 404bp (165410-165814)
>
> position 165410
> length 404
> type MCVc
> comment 'gff3str=.'
>
> <image.png>
>
> and as for A3, it has no coverage at a position of 165209 with a missing
> length of 827bp (165209-166036)
>
> position 165209
> length 827
> type MCVc
> comment 'gff3str=.'
>
> <image.png>
>
> 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.
>
If both of the genomes are mapped to the same reference sequence, you could
make sam and then bam files from each assembly, merge them with picard-tools'
bam merge tool, and then view the merged assembly in Tablet. That way you can
see each of the read groups, and their relationship to the reference sequence.
J
Other related posts:
