TAMALg: is the package available?

I’ve received a lot of questions recently about TAMALg availability. Unfortunately, there is only a difficult-to-install package available right now; I sent it to someone recently and they had a terrible time getting it going.
I do describe the algorithm in the supplementary materials to the ENCODE spike-in competition paper (Johnson et al, Genome Research 2008).
I [...]

Commentary: ChIP-chip vs ChIP-seq and $$

Ok, so with the rush to ChIP-seq and all the hype (much of it deserved) around “next-generation” sequencing generally, you might think that arrays are dead as used for ChIP (i.e. ChIP-chip).
I don’t think this is going to happen for simple cost reasons. For the near future, there will be lots of genome-scale ChIP studies [...]

Viewing Large Text Files (like big GFF files) in Windows

I know, I know, many of you will say “just use Linux”. And this is true, but SignalMap from NimbleGen, which is quite convenient for viewing GFF files of ChIP-chip data, is just a windows product (and yes, I did try WINE as an emulator).
So if you try to load a 380,000 line file into [...]

TAMALPAIS and promoter arrays

TAMALPAIS NimbleGen Promoter Arrays Array Analysis Problems Mark Bieda
I’ve been receiving some questions on TAMALPAIS usage for promoter arrays via email.
On the TAMALPAIS website, I say “Do not use this for promoter arrays.“
This is actually not quite true; there are a limited number of cases in which TAMALPAIS will perform well for promoter arrays. In [...]

On the promoter array analysis server

NimbleGen Promoter Arrays Mark Bieda server Analysis
Note: minor corrections on June 9, 2008
The promoter array server is located at this site
IMPORTANT USAGE NOTE: USE FIREFOX (Internet explorer appears to create issues)
What does it do?
1. This does a simple list comparison using NimbleGen .tab files
In other words, it just outputs the number of entries that are [...]

TAMALPAIS known limitation: must be by chromosome

TAMALPAIS Mark Bieda
TAMALPAIS KNOWN LIMITATION:
1. The first field of the gff file must be by chromosome; in particular, it probably needs to be like chr1
or like chr1, chrX, chrY, chr20.
Further details:
I suspect (but am not sure) that anything of the form chr(anything) will work. But I am not sure of this. Note that use of [...]

TAMALg and TAMALPAIS: NimbleGen data analysis

Ok, I wanted to write about the relationship between TAMALPAIS and TAMALg.
keywords: Mark Bieda, TAMALPAIS, TAMALg, NimbleGen, ChIP-chip
Background
A major part of my research is developing algorithms and statistical models for analysis of ChIP-chip experiments – specifically those done with NimbleGen arrays.
TAMALPAIS (available here) predicts binding sites from NimbleGen array data and also does some basic [...]

TAMALPAIS: howto open files

key words: TAMALPAIS, NimbleGen, Mark Bieda, ChIP, server
Background:
TAMALPAIS is the webserver that I created to analyze NimbleGen ChIP-chip data (note that it is not for promoter data). You can find it at:
http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/tamalpais.cgi
I’ve received queries from a number of people on opening files from my TAMALPAIS server.
Some people have trouble opening the files from the TAMALPAIS [...]