[mira_talk] Re: no singletons in 454 assembly
- From: Isabelle Lesur <isabelle.lesur.kupin@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 8 Oct 2012 16:29:40 +0200
Hi,
Do you have a file with the extension "debrislist" in the .info output
directory. Last time I used MIRA, it is the place I found the list of my
singletons (not the sequence; just the IDs). looks like MIRA calls
"singletons" "debris".
Isabelle
2012/10/8 Peter Menzel <pmenzel@xxxxxxxxx>
> Hi.
>
> I am using mira 3.9.4 for assembly of 454 reads from some metagenomes.
> So far, mira makes makes longer contigs than Newbler, but for some reason
> mira seems to never report singleton reads (neither in the
> *.info_assembly.txt file nor in the *.unpadded.fasta output files).
> So I wanted to ask if this is a known behaviour or maybe a bug?
> For example, one data set contains 707,206 reads and newbler has
> 110,635 singletons and Celera has 46,346 singletons left.
> Mira reports:
> Num. reads assembled: 645541
> Num. singlets: 0
> So there must be some reads left as singletons?
> The file *_info_debrislist.txt has 132545 entries.
>
> I found similar behavior for other 454 assemblies as well.
>
> thanks, Peter
>
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