[mira_talk] Re: 90% Roche454 reads going to debris file...help please !!
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 6 Oct 2011 22:58:01 +0200
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.
Other related posts:
