[mira_talk] Re: no singletons in 454 assembly
- From: Peter Menzel <pmenzel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 8 Oct 2012 17:05:26 +0200
Hi,
ah I didn't see those params.
If you would have a script to give the names of unused reads /
singletons, then I would like to have it :)
Then I can use this list of names to extract the reads from the
original sff file with the sfffile command (like I do with Newbler).
Would that be the same as the debris list as Isabelle suggested?
thanks, Peter
On 8 October 2012 16:40, visam <teutara@xxxxxxxxxxx> wrote:
> 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
>
> --
> You have received this mail because you are subscribed to the mira_talk
> mailing list. For information on how to subscribe or unsubscribe, please
> visit http://www.chevreux.org/mira_mailinglists.html
>
>
>
>
> --
> Quand l’injustice devient la loi, la résistance devient un devoir.
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
