[mira_talk] Re: Illumina paired and merged reads
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 18 May 2014 22:59:35 +0200
On 18 May 2014, at 15:52 , <Theo.Allnutt@xxxxxxxx> <Theo.Allnutt@xxxxxxxx>
wrote:
> is there a way I can denovo assemble Illumina paired data (forward and
> reverse) and a separate file of pairs that have been merged with the program
> 'Pear’:
Simply add them as separate data file in the same readgroup as the unmerged
pairs. MIRA will see them as singlets and not really care that they are in a
pair group.
data = unmerged_1.fastq unmerged_2.fastq merged.fastq
> Also, do you think there is any benefit in doing this, or would Mira itself
> idenitfy the pairs that can be merged by their overlap?
In theory, there should be no benefit. In practice, several people have shown
that there is. I am still somewhat concerned when doing this as, again in
theory, there is a definite non-zero possibility that the pair joining will
create wrong joins within microrepeat areas. Then again … practice beats theory
:-)
B.
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