SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
rmdup can not move duplicates in forward and reverse strand for single-end reads ct586 Bioinformatics 4 03-11-2012 06:01 PM
Forward adapter at end of forward paired end read? darthsequencer Illumina/Solexa 1 03-04-2012 02:37 PM
how to define a forward or reverse read file poorphd Illumina/Solexa 3 11-22-2011 01:34 PM
Average Read Coverage for 454 paired end read data lisa1102 Core Facilities 8 10-18-2011 09:40 AM
bias in mapped forward/reverse read ratios dvh Illumina/Solexa 8 10-02-2008 08:32 AM

Reply
 
Thread Tools
Old 09-06-2012, 07:38 AM   #1
gen_argentino
Junior Member
 
Location: Buenos Aires

Join Date: Sep 2012
Posts: 1
Default MetaSim: why paired end reverse read is much shorter than forward read??

Hi everyone! I'm new here...

I simulated a library paired end 20 kb for 454 technology using MetaSim... but always the reverse read is so much shorter than forward read (forward average: 300 pb and reverse average: 50 pb)

Somebody have any idea why???

I checked the preset of the program and it looks right... so, I don't get it!

Preset Name: 454
Number Of Reads / Mate Pairs=100000
Error Model=454

454 Error Model Configuration=
Number Of Cycles: 137 (~349 Base Pairs)
Mate Pair Probability: 0.99
Mate Pair Read Length: 350
Remove Mate Pair Linker from Output: true
Lognormal Distribution Mean: 0.23
Lognormal Distribution Std. Deviation: 0.15
Proportionality Constant for Std. Deviation: 0.15
Scale Std. Deviation with Square Root of Mean: true
Generate Signal Trace: false

454 Error Model DNA Clone Parameters=
Distribution: Normal
Mean: 20000.0
2nd parameter: 3000.0

Combine All Files=false
Uniform Sequence Weights=false
Number Of Threads=4
Write FastA=true
Compress Output Files=false

regards!!
gen_argentino 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 08:18 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO