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Forum: Bioinformatics 10-02-2017, 08:05 AM
Replies: 0
Views: 283
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: 19,178
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: 1,523
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: 5,766
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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