SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
De novo DNA motif search sikidiri General 9 12-08-2011 05:03 AM
De novo transcriptome assembly and SNP study with redundant PE reads mcastro RNA Sequencing 1 10-22-2011 03:40 PM
Input parameters GS de novo Assembler grassgirl 454 Pyrosequencing 0 06-03-2011 11:40 AM
SNP detection (no reference) parameters extari De novo discovery 0 05-09-2011 07:42 AM
MIRA transcriptome assembly and isoforms JueFish Bioinformatics 5 02-02-2011 08:34 PM

Reply
 
Thread Tools
Old 02-03-2010, 04:50 AM   #1
macoma
Junior Member
 
Location: France

Join Date: Jan 2010
Posts: 1
Default mira parameters for SNP search in transcriptome de novo

Hi
I have 3 populations that are tagged. Ten individuals (non tagged) within each populations.
We used 454 titanium technology, with non normalized cDNA bank
The aim of our study is to select SNP in order to make a genome scan (Fst scan) to found selection.
I choose Mira for the assembly, but I'm not sure to use it properly.For the moment I made assemblies with default parametres of miraESTSNPs -job=denovo,est,454. I just test modifying -AL: mrs (default = 80, test = 70 and 90), -AL:ms (default=15, test 10 and 20).
For information the average expected identity between 2 alleles is something like 95%.
I need a good coverage because to validate a SNP it has to be present at least 10 times (20 times would be better).
There are a lot of parameters we can modify but I'm not sur to really know on what parameters I have to focus on for my study.
Somebody could give me some advice ?

For information :
few stats : default parameters + ms=10
Num. reads assembled : 360376
Num. singlets : 4008
Num. contig >=500 bases : 5945
Total consensus: 5677061
MAx coverage : 842
avg. coverage = 11,53
few stats : default parameters
Num. reads assembled : 360240
Num. singlets : 4008
Num. contigd >=500 bases : 9119
Total consensus: 8368209
MAx coverage : 840
avg. coverage = 8,73
few stats : default parameters + ms=20
Num. reads assembled : 360103
Num. singlets : 3936
Num. contig >=500 bases : 6001
Total consensus: 5724129
MAx coverage : 795
avg. coverage = 11,87
few stats : default parameters + mrs=90
Num. reads assembled : 308455
Num. singlets : 4039
Num. contig >=500 bases :0
Total consensus: 0
MAx coverage : 0
avg. coverage = 0
few stats : default parameters + mrs=70
Num. reads assembled : 383220
Num. singlets :7495
Num. contig >=500 bases :16355
Total consensus: 14075898
MAx coverage : 851
avg. coverage = 6,27
macoma is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:47 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO