[mira_talk] Help with MCVc (missing Co Verage in consenus) after mapping assembly

  • From: Austen Chen <cyausten@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Tue, 4 Feb 2014 12:53:29 +1030

Hi Bastien,

we have done 2 mapping aseemblies (A1 and A3) using a common bacterial
reference, and now we need to find regions that are missing in either
strain or common to both A1 and A3. 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=.'

For A3
position 165209
length 827
type MCVc
comment 'gff3str=.'

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)

[image: Inline image 1]

because these positions are in relation to their own contigs, it's
impossible to compare A1 and A3 to see if they have common missing regions.
It would be straightforward if the positions are given in reference to the
reference strain, then common missing regions would have the same
coordinates.

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.

thank you so much in advance

Austen

PNG image

Other related posts:

  1. Home
  2. mira_talk
  3. Archive
  4. 02-2014