[BioC] Query

[michael watson (IAH-C)]

I believe maq has the facility to simulate NGS reads

http://maq.sourceforge.net/
________________________________________
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Yogesh Kumar [yogesh.srmc at gmail.com]
Sent: 24 February 2010 05:43
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Query

Respected Sir/Madam,

Good morning, I just started my PhD in Next generation sequencing datasets..
I have one query , can you help me to handle this query.

we  have sequence of 1MB region from Human chr 22 (haploid). we want to cut
the length of max 450-500bp  ( given use Normal distribution, Mean 500 and
SD=?). *I want to know how can we generate reads from our sequence*   (
paired end of 75bp at both ends, Assuming  perfect reads). we want to do
simulation of NGS run and reassemble it  again  without using reference
sequence. Can we use R for simulation work also? if yes please provide me
which package we can use for it and possible send me R script too.

1. To establish simulation of reassembling sequence from NGS data. This will
build from re-assembling a simple sequence of 1 Mb with no repeats in the
haploid state, to inclusion of genetic variation and polyploidy.
       -simulate a NGS run from a 1 Mb segment of human with little/no
repeats. Average fragment size 500 bp with normal distribution. Paired end
with 75 bp reads. Assume perfect sequencing. Check out other simulation
methods
       - align the reads back to the 1 Mb sequence. How much variation in
coverage
       - reassemble the reads WITHOUT using the reference sequence.




http://maq.sourceforge.net/maq-manpage.shtml#7

I think we can use above link but not be able to work out . can you check it
and send me solution

Regards
Yogesh Kumar
University of Otago
Dunedin, NZ
0064226149242

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