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Search: Posts Made By: konrad98
Forum: Academic/Non-Profit Jobs 05-19-2013, 06:03 AM
Replies: 0
Views: 990
Posted By konrad98
Exeter Sequencing Service, UK - Bioinformatic and Software Development Post

The University of Exeter Sequencing Service wishes to recruit an Experimental Officer to provide software development, informatics support and pipeline development...
Forum: General 07-13-2011, 07:44 AM
Replies: 10
Views: 2,960
Posted By konrad98
It would also be helpful if the authors could...

It would also be helpful if the authors could post which versions of reagents were used for sequencing - especially with the Illumina results. 9 million reads from 2 lanes is indicative of very old...
Forum: Bioinformatics 06-20-2011, 03:47 PM
Replies: 6
Views: 2,485
Posted By konrad98
As Nick alluded, a single type of library will...

As Nick alluded, a single type of library will never give you as good an assembly as a mix of different insert sizes and read lengths. However single-end reads should be enough to give you most genes...
Forum: Ion Torrent 03-25-2011, 02:48 AM
Replies: 34
Views: 12,979
Posted By konrad98
Hmmmm...... Iago

Hmmmm...... Iago
Forum: Illumina/Solexa 01-12-2011, 11:43 AM
Replies: 13
Views: 6,180
Posted By konrad98
A year or two ago Illumina were talking about...

A year or two ago Illumina were talking about producing an ordered flowcell so that you could pack more clusters in using technology borrowed from some of their other products.

I imagine Illumina...
Forum: Illumina/Solexa 01-12-2011, 11:35 AM
Replies: 74
Views: 47,526
Posted By konrad98
kmcarr - I think James was referring to lanes. A...

kmcarr - I think James was referring to lanes. A PE lane on a GAII will yield around 70-80 million reads. If the MiSeq yields 7 million per run then the numbers look fine.
Forum: Illumina/Solexa 09-29-2010, 04:07 AM
Replies: 18
Views: 6,339
Posted By konrad98
Beyond 800bp you start getting cluster sizes...

Beyond 800bp you start getting cluster sizes which are almost guaranteed to merge with each other during the course of a run. You can can get around this by lowering the cluster density to around...
Forum: De novo discovery 08-11-2010, 02:34 PM
Replies: 10
Views: 9,202
Posted By konrad98
In my experience I have found that minimus2...

In my experience I have found that minimus2 converts all Ns to As.
Forum: RNA Sequencing 08-11-2010, 09:47 AM
Replies: 3
Views: 3,791
Posted By konrad98
Under the contrib/extractContigReads directory in...

Under the contrib/extractContigReads directory in Velvet you'll find a script to do this
Forum: RNA Sequencing 08-10-2010, 12:44 PM
Replies: 28
Views: 12,164
Posted By konrad98
Hi thinkRNA, In cufflinks I am using a...

Hi thinkRNA,

In cufflinks I am using a reference annotation which contains only a few splice variants (no more than 100). Of those that are there, there doesn't seem to be any relationship...
Forum: RNA Sequencing 08-10-2010, 03:03 AM
Replies: 3
Views: 3,791
Posted By konrad98
Hi Simon, I'm not by any means an expert on...

Hi Simon,

I'm not by any means an expert on this, but you probably have two options:

1. Convert the kmer coverage in the stats.txt file to base-coverage and use that as a proxy for expression...
Forum: RNA Sequencing 08-06-2010, 02:52 AM
Replies: 28
Views: 12,164
Posted By konrad98
Hi xinchen, The htseq counts and the FPKM...

Hi xinchen,

The htseq counts and the FPKM counts have reasonably good agreement. (R^2=0.9), so I don't think this would explain the more than a fraction of the discrepancy.

Cole - if you have...
Forum: RNA Sequencing 08-05-2010, 06:55 AM
Replies: 28
Views: 12,164
Posted By konrad98
I can't say if its common or not, but its only a...

I can't say if its common or not, but its only a problem I encounter with Cufflinks. When using DESeq and edgeR it won't classify such genes as being differentially expressed so I don't perform any...
Forum: RNA Sequencing 08-05-2010, 05:10 AM
Replies: 28
Views: 12,164
Posted By konrad98
Hi all, Many thanks for your speedy...

Hi all,

Many thanks for your speedy response!

I have supplied cuffdiff with serval GTF files for comparison:

1. The output from cuffcompare (i.e. the stdout.combined.gtf file) when the...
Forum: RNA Sequencing 08-04-2010, 11:50 AM
Replies: 28
Views: 12,164
Posted By konrad98
Tophat, Cufflinks and replicates

Hi all,

I've analysed a series of 2 pairs of different biological replicates with 3 programs, Cuffdiff, DESeq and edgeR. At the moment I'm just looking at gene-level expression.

One would...
Forum: Service Providers 09-11-2009, 04:21 AM
Replies: 162
Views: 153,482
Posted By konrad98
Exeter, UK ...

Exeter, UK

http://biosciences.exeter.ac.uk/genome_analyser/
Forum: Illumina/Solexa 04-29-2009, 04:47 AM
Replies: 4
Views: 2,173
Posted By konrad98
Angry Delivery delays - is anyone else suffering

Hi all,

We have had our GA2 for 6 months now and on several occasions we have had delays of up to a month or more on our reagent deliveries.

Quite often these delays are not communicated until...
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