MetaSim: why paired end reverse read is much shorter than forward read??

gen_argentino · 09-06-2012, 07:38 AM

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!!

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

09-06-2012, 07:38 AM	#1
gen_argentino Junior Member Location: Buenos Aires Join Date: Sep 2012 Posts: 1	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!!