[mira_talk] Re: Help with MCVc (missing Co Verage in consenus) after mapping assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 4 Feb 2014 08:21:48 +0100
On 04 Feb 2014, at 3:23 , Austen Chen <cyausten@xxxxxxxxx> wrote:
> […] we used a tag called MCVc to locate missing regions using Gap4. we were
> able to find all these missing regions in each strain and each missing region
> was given as a position (see below).
>
> For A1
> position 165410
> length 404
> type MCVc
> comment 'gff3str=.’
I’m not sure I I’m interpreting this right, but I’m going to assume you made a
mapping, imported that into gap4, made some edits/finishing there and then
exported the tag positions from within gap4. Am I right?
> […]
> but then we realised these positions are given in reference to each contig A1
> and A3, not in reference to the common reference strain. see below (A1-top,
> A3-bottom)
If yes, then this does not work (as you experienced) because gap4 has no notion
of “reference sequence”.
Way out: convert the gap4 database back to CAF, then use “miraconvert -t
cstats” to recreate info files like MIRA gives at the end of a sequencing run.
There you can use the “unpadded” positions. At least I hope so. If not,
converting to SAM and using the positions there might help.
> […]
> We need to get this work done urgently so any advice you could give us on the
> best way to solve this problem would be greatly appreciated.
Sending a mail to the MIRA talk list at 03:23 MET, not getting a response and
then sending me a mail to my private address at 06:14 MET usually is not
helpful. Just saying.
B.
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