[mira_talk] Re: I need help understanding the contigs with suffix "_rep_c"

  • From: Pau Corral <pau.corral@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 12 Oct 2011 17:52:39 +0200

I follow this thread,

So essentially, what one can find in this file
/projName_assembly/projName_d_results/projName_out.unpadded.fasta
is two type of consensus sequences (at least this is what I have in my
executions):

1)>projName_c[number]
2)>projName_rep_c[number]

What is the difference between these two types of consensus sequences?
Is this explained elsewhere?

Excellent documentation here:
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html
Congratulations!!

Pau

On Wed, Sep 14, 2011 at 9:13 PM, jyotsna guleria
<jyotsna.guleria@xxxxxxxxx>wrote:

> Thanks a lot !!
>
> Jyo
>
>
> On Wed, Sep 14, 2011 at 3:10 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>
>> On Sep 13, 2011, at 22:38 , John Nash wrote:
>> > They are contigs with regions which are repeated in other contigs (or
>> other areas within a contig) with insufficient flanking information to join
>> them elsewhere. Essentially, misassembled paralogs.
>> >
>> > What the regions should look like:
>> >
>> > Region 1: --- flank L1 ---- REPEAT ---- flank R1
>> > Region 2: --- flank L2 ---- REPEAT ---- flank R2
>> > Region 3: --- flank L3 ---- REPEAT ---- flank R3
>> > Region 4: --- flank L4 ---- REPEAT ---- flank R4
>> >
>> > Ideally, the above four regions lines should assemble into separate
>> paralogs within one or more contigs.
>> >
>> > What the rep contigs contain:
>> >
>> > Region: --- [mix of flank L1, L2, L3, L4] ---- REPEAT ---- [mix of flank
>> R1, R2, R3 and R4] ---
>>
>>
>> Actually, the above should never be the case because the flanks should be
>> assembled with their respective contigs. Although it might happen in very
>> rare cases.
>>
>> The rep contigs ideally look like this:
>>
>> Region:  ---- REPEAT ----
>>
>> It cannot be completely excluded that some remnants of the flanking
>> sequences remain, in those cases however it is much more probable to have
>>
>> Region: --- [any of flank L1, L2, L3, L4] ---- REPEAT ---- [any of flank
>> R1, R2, R3 and R4] ---
>>
>> and not a mix.
>>
>>
>> B.
>>
>>
>> --
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>
>

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