[mira_talk] Re: 90% Roche454 reads going to debris file...help please !!
- From: jyotsna guleria <jyotsna.guleria@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 6 Oct 2011 18:01:56 -0400
I tried what you suggested still it didn't work.. :(
Here is the new logfile with changes:
http://dl.dropbox.com/u/10010521/logfile
Kindly help !
Thanks,
Jyotsna
On Thu, Oct 6, 2011 at 5:11 PM, jyotsna guleria
<jyotsna.guleria@xxxxxxxxx>wrote:
> Thanks so much !!
>
> So, you suggest I should not use -SK:nrr=10 for 4k reads?
> Can you suggest a range to use this option? e.g can I use it if I have 10k
> reads or more?
>
> For your question: any special reason you switch of proposed end clipping?
> (-CL:pec=no)
>
> We had a discussion about it long back where I mentioned that for some
> reason if I turn ON this option of clipping I get more debris...don't know
> why but it did happen and from then I have been assembling reads with same
> command and never had any trouble so far...!
>
>
>
> Many thanks for the help!
>
> Jyotsna
>
>
> On Thu, Oct 6, 2011 at 4:58 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>
>> **
>>
>> On Thursday 06 October 2011 18:07:28 jyotsna guleria wrote:
>>
>> > Can someone please help me in understanding what is going wrong by
>> looking
>>
>> > at the logfile uploaded at :
>>
>> > All of my reads are going into debris list, I am not able to understand
>>
>> > why....
>>
>>
>>
>> 1. wrong command line. Do not write
>>
>> mira --project=... --job=... [some options] --highlyrepetitive ...
>>
>> but
>>
>> mira --project=... --job=... --highlyrepetitive [other options] ...
>>
>>
>> "--highlyrepetitive" is a position dependend parameter, look that up in
>> the documentation.
>>
>>
>>
>> 2. any special reason you switch of proposed end clipping? (-CL:pec=no)
>>
>>
>> 3. -SK:nrr=10 might be one cause for your problem. Almost every read has
>> some
>>
>> kind of probelamtic stretch, see the log line:
>>
>>
>> "Writing read repeat info to:
>>
>> JCV345MDA_assembly/JCV345MDA_d_info/JCV345MDA_info_readrepeats.lst ...
>>
>> 3289 sequences with 8201 masked stretches."
>>
>> Such a tiny project with 4k reads does not need that.
>>
>> 4. Only 1/3 of the reads is finally used in the assembly. See log lines
>>
>> Building new contig 1
>>
>> Localtime: Thu Oct 6 16:23:12 2011
>>
>> Unused reads: 1514
>>
>> The rest did not have any kind of overlaps. See again -SK:nrr
>>
>> B.
>>
>
>
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