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Search: Posts Made By: pederworning
Forum: General 09-09-2021, 06:16 AM
Replies: 1
Views: 2,249
Posted By pederworning
Red face SNP Bacterial Genomes per year

I am looking at SNP trees for bacterial genomes (mostly N. gonorrhoeae, S. aureus and E. faecium) and I am following outbreaks in society and on hospital wards.
Do you know the number of SNPs that...
Forum: Bioinformatics 10-02-2017, 08:05 AM
Replies: 0
Views: 1,199
Posted By pederworning
Unhappy Gviz Installation

Hello I am using R 3.2.3 on ubuntu 16.04 LTS and I can't the R package Gviz

I have done the following:

source("https://bioconductor.org/biocLite.R")

biocLite("Gviz")

I think the problem...
Forum: 454 Pyrosequencing 09-09-2011, 03:49 AM
Replies: 30
Views: 23,877
Posted By pederworning
Thanks for the installation instructions, if you...

Thanks for the installation instructions, if you have java installed you need to make a link to /bin/java
to make it run:
$ which java
/usr/local/bin/jre1.6.0_24/bin/java
/bin$ sudo ln -s...
Forum: Bioinformatics 06-23-2011, 04:42 AM
Replies: 1
Views: 2,296
Posted By pederworning
VelvetOptimiser sam format

Dear Bioinformatic forum,

I am using VelvetOptimiser to see which parameters to use for Velvet denovo assembly, but I cannot get it to read sam files. It can read fasta and fastq but not sam.
I...
Forum: Bioinformatics 04-08-2011, 08:04 AM
Replies: 4
Views: 9,481
Posted By pederworning
samtools sort stdout

Hello

I am mapping reads from bacterial sequences to reference genomes and I am using bwa and samtools. I am trying to set up a pipeline and want to use stdin and stdout and pipe the data to...
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