[mira_talk] Re: Make us check a part of results

On 09/06/16 6:35 AM, Bastien Chevreux wrote:

On Montag 15 Juni 2009 Kenta SHIRASAWA wrote:

1)
   We will use a mira_out.txt output for a further analysis. We are
happy if MIRA makes a result txt file one by one contig, or adds a
created contig to a result txt file, because we can check a part of
results without waiting for finishing whole assemblings.
Well, MIRA has no other possibility ... to save memory, contig structures get freed and re-allocated once a contig has been finnished. The update of the files on the fly is merely a (very welcome) side effect :-) 

We are checking the caf file before finishing the assemble.




2)
   Can you estimate how long time does MIRA take for finishing an
assemble 500,000 454-reads (ca. 200 Mb) with the options "-fasta
-job=denovo,est,draft,454 -notraceinfo -SB:lsd=yes -SK:pr=95 -SK:mnr=yes
-OUT:ort=yes"?
   Our machine (64bit linux, 2 GHz CPU, 128 GB memory) has been running
for more than a week.
Something's wrong there, plain wrong. May I ask you to send me the output log of the assembly to have a look at?
We have checked our EST 454-reads, and are surprised that about 20% reads were classified as "repeat". Such reads might come from highly expressed transcripts. MIRA could run much faster after removing the reads. 


3)
   Please tell us a difference between conting headers, e.g., mira_c#
and mira_lrc#.
I really need to document that: it's a remainder of larger changes that are currently made in the algorithms, it was introduced more for debugging purposes but a few users thought it could help them so I left it in.
Basically, MIRA starts to build contigs in areas that are "rock solid", i.e., not a repetitive region (main decision point) and nice coverage of good reads. If during the assembly MIRA reaches a point where it cannot start building a contig in a non-repetitive region, it will name the contig "lrc" instead of "c".
Of course, this naming convention is a bit weird (not to say: useless) when having to assemble ESTs, but at the moment I didn't build in code that switches of contig naming in these cases. 



I understood.

Thank a lot Bastien, Lionel, and Jan.

Regards,
Kenta Shirasawa

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