[mira_talk] Re: no singletons in 454 assembly
- From: visam <teutara@xxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 8 Oct 2012 17:40:34 +0300
Hi Peter,
MIRA will output singlets if you enable -out:stsip=1:sssip=1
(savesimplesingletsinproject, savetaggedsingletsinproject) parameter, into
the contig output file (*.unpadded *.padded) with _s suffix.
But, i suggest you use a script such as listing used read list from .ace
file (or whatever other file) and filter those from raw reads.
I wrote such a script -java-, if you can not manage, let me know, i can send
it.
Best,
Visam
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx]
On Behalf Of Isabelle Lesur
Sent: Monday, October 08, 2012 5:30 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: no singletons in 454 assembly
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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