Comments for Back of a Stamp

Comment on IoP Collaboration graph with R igraph by cass

cass — Wed, 28 Jul 2010 22:56:55 +0000

Hey Christian – probably a bit late now, but I’ve added a link to the code.

Comment on IoP Collaboration graph with R igraph by christian

christian — Wed, 09 Jun 2010 12:56:59 +0000

Hi!

Trying to learn how to use the igraph package in R I came across your beautiful graph. Great, inspiring work!

I tried to do something similar, but sofar I haven’t succeeded. Could you give me hint about the source code of this graph?

All the best,

Christian

Comment on ffmpeg: Unknown encoder ‘mp3′ by karuppasamy

karuppasamy — Thu, 08 Oct 2009 06:25:26 +0000

Thanks for Your Information. it is really use for me..

Thanks & Regards
P.Karuppasamy

Comment on ELAND by cass

cass — Thu, 10 Sep 2009 12:10:48 +0000

Ah, ok, thanks! So, the original ELAND aligns as above,and chucks out anything that aligns in multiple places. The extended one does the same thing, but hangs on to multiple matches and then runs a second stage where it looks to see which of the 32b seed alignment positions have the best alignment with the full read length? Presumably it then chucks out anything that *still* matches in multiple places?

Comment on ELAND by Maria

Maria — Wed, 09 Sep 2009 12:48:27 +0000

Hi Caroline,
Can you get additional information from the Illumina website if you have an Illumina user account?

This is what I got from an Illumina user guide that someone posted on SEQanswers:

ANALYSIS eland_extended is an improved version of the ANALYSIS eland
mode. ANALYSIS eland can align reads longer than 32 bases but demands
that the first 32 bases of the read have a unique best match in the genome.
The position of this match is used as a “seed” to extend the match along the
full length of the read. ANALYSIS eland_extended removes the uniqueness
restriction by considering multiple 32 base matches to be considered and
extended.

Maria

Comment on Illumina fastq format / quality score confusion by cass

cass — Fri, 07 Aug 2009 21:54:49 +0000

Hi Maria!

Glad it’s useful. Just be warned that I’m not 100% sure it’s all correct – it’s just what I’ve gleaned from the various bits of documentation I can get my hands on and a couple of frustrating days Googling.

Comment on Illumina fastq format / quality score confusion by Maria

Maria — Fri, 07 Aug 2009 11:51:39 +0000

Very helpful. I’ve been trying to learn about the output files by reading the Illumina manual but hadn’t got this far yet.

Comment on Illumina fastq format / quality score confusion by LaviniaG

LaviniaG — Wed, 05 Aug 2009 03:42:08 +0000

Useful info – thanks – keep up the posting.

Comment on ffmpeg: Unknown encoder ‘mp3′ by malc

malc — Wed, 22 Jul 2009 11:01:34 +0000

THANK YOU! Yes it robbed me of more than 20mins of my life.
I tried mp2 but got:
Warning, using MS style audio codec tag, the file may be unplayable!
and with mp3:
Unknown encoder mp3

Bah! – thanks again for destressing my day!
Malc.

Comment on Setting up Galaxy by cass

cass — Wed, 08 Jul 2009 14:31:27 +0000

They gave us a grant, so it’s currently free. I need to work out how we’re going to use it in the long term though.

For doing data analysis, it’s much easier than booking time on a cluster at work, as I can install exactly what I want without having to go through the cluster admin and I don’t have to wait in line. Unless we start doing a lot more data analysis, I think it’s still going to work out much cheaper than buying in our own hardware and it’s certainly going to be less hassle. I’m envisaging just running instances of the Galaxy and analysis AMIs when we’re actually doing the alignment, peak finding and so on. I’ll probably keep the short read data as BAM or BioHDF on S3 so people can get at them and run their own analysis on EC2 if they want to.

I also need to set up a LIMS-type server for managing and sharing our data. Probably with some kinda REST-API so other stuff (network building tools etc) can query the data (eg. “What experiments have you done that involve NRSF? as RDF?” or “Give me all the features between these chr co-ords for NRSF binding in NS5 cell lines as BED, or SAM or something). We can host this kind of thing at work and it doesn’t really need to scale much. So I imagine I’ll have the analysis pipeline hand me back a list of peaks (genome pos, plus score, pvalue etc) and some metadata describing the analysis workflow and dump that into my LIMS thing.

I’ll bring my laptop to the biogeeks thing if you want to have a play with the AWS stuff.

I guess I’ll probably just stick the short read data onto EC2 for analysis and have it spit out the binding peaks and analysis metadata back to me.