[mira_talk] Re: Solexa paired ends and 454 single reads

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.

Thanks,
Mihaela

-----Original Message-----
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Lionel Guy 
Sent: Donnerstag, 21. Jänner 2010 10:17
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Solexa paired ends and 454 single reads

Hi Mihaela,
I've been running such an assembly. Whereas the 454-only (~300k reads) assembly took a few hours, adding ~500k Solexa paired-end reads made it about 8 days... I think this is due to the fact that building contigs is highly time-consuming in MIRA, and Solexa reads assemble in a lot of small contigs. 

You can check what Pass MIRA is in:

grep "Pass" assembly.log

As far as I remember, MIRA does 5 passes when set with accurate.
By the way, how many reads of each kind do you have?

Cheers,

Lionel

On 21 Jan 2010, at 10:08 , Mihaela Angelova wrote:


Hello,
I want to use Mira for assembly of 454 reads combined with solexa paired end reads. However, the assembling was started two days ago 
with:
mira -project=pp -job=denovo,genome,accurate,454,solexa -GE:amm=no SOLEXA_SETTINGS -GE:tismin=2500:tismax=3500
and still hasn't finished. 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. 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? Is it normal that the run takes more than two days (if i need half a day to assemble the 454 reads without the paired ends)? 
Thanks a lot,
Mihaela



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Lionel Guy
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phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy.lionel@xxxxxxxxx
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