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Forum: Bioinformatics 03-07-2011, 12:45 AM
Replies: 0
Views: 2,187
Posted By peveralldubois
Global Alignment With Mummer (Parameter for Gap Extension & Opening Cost)

Dear Sir,

I am trying to perform global alignment for contigs to several
chromosomes in genome using Mummer.

I am wondering what is the parameter I can use for setting the parameter below

Forum: Bioinformatics 02-12-2011, 04:58 PM
Replies: 1
Views: 2,154
Posted By peveralldubois
MAQ Simulator SNP/Indel Output

One of the output generated by maq simulate (haploid mode)
looks like this:

chr22 16068102 C M +
chr22 16068255 A R +
chr22 16069235 G ...
Forum: Bioinformatics 01-14-2011, 08:23 PM
Replies: 0
Views: 2,129
Posted By peveralldubois
Extract Gap and Mismatch From MAF alignment Output

Dear Experts,

Is there any tools that extract gap and mismatch From MAF alignment output
as well as identifying the position where the mismatch happen both in target and query sequence.

Forum: Bioinformatics 01-13-2011, 05:54 AM
Replies: 4
Views: 2,865
Posted By peveralldubois
Hi Yilong, Thanks so much for your reply. ...

Hi Yilong,

Thanks so much for your reply.
I tried to run 'fakemut' from maq using this command.

maq fakemut chr22.fa > out.fakeref.fasta 2> out.fake.snp

Do you know what does each column...
Forum: Bioinformatics 01-13-2011, 01:41 AM
Replies: 4
Views: 2,865
Posted By peveralldubois
Generic SNP/Indel Simulator for NGS data

Expert is there any existing SNP/Indel Simulator for NGS reads?

The principle the tool does something like taking any reference genome, pick positions randomly in that genome and begin to...
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