[mira_talk] Re: Solexa paired ends and 454 single reads
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 21 Jan 2010 20:45:50 +0100
On Donnerstag 21 Januar 2010 Mihaela Angelova wrote:
> Thanks a lot for answering me.
> Mira is still not in any Pass now. The log assembly is stuck at this :
>
> Now running threaded and partitioned skimmer with 272 partitions in 2
> threads: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|....
> [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
> ....|.... [90%] ....|.... [100%]
>
> I have ~668.000 reads (from 454) and ~75.000.000 paired-end reads in total.
Hi Mihaela,
uh, 75m reads? If it's a bacterium, that's far to many. If it's something
larger ... hmm, I don't know why it should take an eternity right there. If
you are interested I can give you a version with a lot of debugging. It won't
help you immediately, but at least I'd have an idea where the problem is.
> I have noticed that a huge number of paired
> ends were discarded because they were too short :
>
> AAA/2 too small even with paired end
>
> Is this because their ends might have been clipped.
Yes, exactly.
> In the project_int_clippings.0.txt there are messages like :
>
> proposed cutback 1b: left AAA/2 9 -> 24
>
> If I use the noclipping command, would it make the run more accurate?
I very, very strongly suggest to use the proposed end clipping (PEC) for data
sets with a coverage >15x (I suppose that to be the case for yours). PEC is
inanely effective in doing in pre-screen and clips extremely effectively
without clipping to much. If you don't use PEC, the assemblies are worse in
95% of the time, especially with Solexa and 454 reads.
The output log gives you an idea how much was really clipped. It looks like
this (example for a project with 800k 454 reads):
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 31737
Num reads cliped right: 131198
Num reads completely killed: 7205
Total bases clipped : 2236490
Should these numbers be extremely high for you, then one should ask why the
dataset is like that.
Regards,
Bastien
--
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:
