[mira_talk] questions about statistics
- From: Dong Zhang <zhangdong20046@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 17 Dec 2009 13:12:37 -0500
Hi Bastien,
I have some questions about statistics after assembly.
Here is the information from “info_assembly.txt”.
Read assembled: 86373
Singlets: 3445
Number of contigs: 7012
The number of reads in the “info_contigreadlist.txt” is 84741.
The number of reads in the “info_debrislist.txt” is 15145
Here is the statistics from result fasta file.
Unigenes with “_c” tag: 6524
Unigenes with “_lrc” tag: 488
Unigenes with “_s” tag: 1813
The following are my questions.
1. What is difference between “read assembled” and reads which are listed in
the “contigreadlist.txt” (86373 != 84741)?
2. It seems that you treat part of debris as singlets (3445 != 15145), and
you didn’t put all of singlets into result fasta file (3445 != 1813). Could
you explain more about this? I used command line as following.
mira -project=CBreton_Region_1_MID22 -fasta -job=denovo,est,normal,454
-notraceinfo -OUT:sssip=yes:ora=yes -AS:ugpf=no:sep=yes:bdq=20
-AL:ms=20:mrs=85:egp=yes -CL:pvlc=no:pvcmla=25:cpat=on:qc=no:qcmq=16:qcwl=20
-ED:ace=yes -SK:not=2:pr=50
Thanks a lot in advance and Best regards,
--Dong
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