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Forum: Bioinformatics 07-05-2011, 08:27 AM
Replies: 0
Views: 2,165
Posted By Jasmine
Simulation package in R

Hi all,

I'm looking for a package or code which can generate artificial reads based on Genome or Transcripts using R.

If anyone knows this, that would be great :)

Jasmine
Forum: Bioinformatics 02-09-2011, 06:19 AM
Replies: 0
Views: 1,551
Posted By Jasmine
What is your trimming strategy?

I've been using Illumina data but the data which I got contain a lot of low quality data.
I tried to set a variety of trimming using quality score. If I set too strict, 70 or 80% of reads are...
Forum: Bioinformatics 07-08-2010, 03:15 PM
Replies: 3
Views: 2,805
Posted By Jasmine
I could find the Illumina Genome Analyzer IIx...

I could find the Illumina Genome Analyzer IIx data by below steps using SRAdb package :) I thought I should share what I did.


source("http://bioconductor.org/biocLite.R")
biocLite("SRAdb")...
Forum: Bioinformatics 07-07-2010, 03:10 PM
Replies: 3
Views: 2,805
Posted By Jasmine
Thank you, this is fantastic. I'll take a look at...

Thank you, this is fantastic. I'll take a look at the package.
Forum: Bioinformatics 07-07-2010, 09:03 AM
Replies: 3
Views: 2,805
Posted By Jasmine
How to search by instrument in SRA?

Hello all,

I'm looking for a public data set which used Genome Analyzer IIx. Does anyone know how to search NCBI SRA site by instrument name?

I'd like to find a data set which use 100bp read....
Forum: Bioinformatics 06-16-2010, 03:17 PM
Replies: 6
Views: 7,619
Posted By Jasmine
Hi RockChalkJayhawk, I think your data...

Hi RockChalkJayhawk,

I think your data doesn't have id.

There is an example of nullp help,

data(prostate)
pwf <- nullp(genes, 'hg19', 'ensGene')

genes object has names,
Forum: Bioinformatics 06-16-2010, 09:12 AM
Replies: 6
Views: 7,619
Posted By Jasmine
Smile Looks like some packages which goseq needs were...

Looks like some packages which goseq needs were not installed properly.

widgetTools seems to be the first package which failed to install. You can find the widgetTools from below site. You can...
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