[mira_talk] Selecting best contigs...
- From: Andrzej N <andrzej.k.n@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 4 Dec 2009 11:34:26 -0600
Hello,
This is my assembly info:
*Assembly information:
=====================
Num. reads assembled: 194398
Num. singlets: 82
Large contigs:
--------------
With Contig size >= 500
AND (Total avg. Cov >= 29
OR Cov(san) >= 0
OR Cov(454) >= 27
OR Cov(sxa) >= 0
OR Cov(sid) >= 0
)
Length assessment:
------------------
Number of contigs: 169
Total consensus: 763757
Largest contig: 48172
N50 contig size: 9852
N90 contig size: 1758
N95 contig size: 1370
Coverage assessment:
--------------------
Max coverage (total): 894
Max coverage
Sanger: 0
454: 900
Solexa: 0
Solid: 0
Avg. total coverage (size >= 5000): 87.13
Avg. coverage (contig size >= 5000)
Sanger: 0.00
454: 88.79
Solexa: 0.00
Solid: 0.00
Quality assessment:
-------------------
Average consensus quality: 78
Consensus bases with IUPAC (IUPc): 446 (you might want to check
these)
Strong unresolved repeat positions (SRMc): 1 (you might want to
check these)
Weak unresolved repeat positions (WRMc): 0 (excellent)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)*
I would like to choose ONLY this 169 contigs to work on it in GAP4. I know
how to choose contigs based on size, but how can I get this 169 contigs in
ONE file?
How does this results looks like... :).
There 894 coverage, this is because there are repeats which pile up on each
other, is there any option to "stop" MIRA of doing it?
Andrzej
I looked on link to your manual, but there is only way of choosing size and
coverage as a selection method...
Other related posts:
