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Search: Posts Made By: pmcget
Forum: Bioinformatics 03-27-2013, 05:09 AM
Replies: 9
Views: 1,538
Posted By pmcget
Also developments in denovo space are moving very...

Also developments in denovo space are moving very quickly with incorporation of long Pacbio reads and Moleculo pseudo-contigs/sub assemblies. Using this type of data it may be possible to revert back...
Forum: Bioinformatics 03-27-2013, 04:51 AM
Replies: 9
Views: 1,538
Posted By pmcget
The Assemblathon project/contest (and related...

The Assemblathon project/contest (and related commentary) is a good indicator of the state of the art in de novo assembly:

http://assemblathon.org/
Forum: Bioinformatics 03-26-2013, 08:07 AM
Replies: 9
Views: 1,538
Posted By pmcget
The reason I made those points was that they...

The reason I made those points was that they directly impact on your proposal:

1. It isn't easy to identify the reads that should be used in a denovo assembly
2. Most of the reads generated are...
Forum: Bioinformatics 03-26-2013, 06:31 AM
Replies: 9
Views: 1,538
Posted By pmcget
Hi yaximik, There are two difficulties I see...

Hi yaximik,

There are two difficulties I see with this suggestion:
1. The contamination of archaelogical samples with other organisms - fungi, bacteria etc - how would you separate novel ancient...
Forum: Bioinformatics 03-21-2013, 06:07 AM
Replies: 6
Views: 2,745
Posted By pmcget
Differing amounts of PolyA almost certainly will...

Differing amounts of PolyA almost certainly will lead to mapping bias.

A quick search found this tool for trimming polyA from FASTQ files:
http://chipster.csc.fi/manual/prinseq-AT-trimmer.html
...
Forum: Bioinformatics 03-21-2013, 02:45 AM
Replies: 6
Views: 2,745
Posted By pmcget
If you want to search a wider range for potential...

If you want to search a wider range for potential contaminants you could use MEGAN:
http://ab.inf.uni-tuebingen.de/software/megan/
Forum: Bioinformatics 03-21-2013, 02:42 AM
Replies: 6
Views: 2,745
Posted By pmcget
Do you have the same read lengths for the control...

Do you have the same read lengths for the control sample - or are they shorter?
Forum: Bioinformatics 02-27-2013, 02:24 AM
Replies: 8
Views: 3,473
Posted By pmcget
Hi inesdesantiago, I think chipper is...

Hi inesdesantiago,

I think chipper is correct.

If you want to graphically investigate it further you could identify all the windows with a substantial repeat overlap e.g. using BEDtools...
Forum: Bioinformatics 02-26-2013, 06:03 AM
Replies: 8
Views: 3,473
Posted By pmcget
Is it possible that your peaks are enriched for...

Is it possible that your peaks are enriched for repetitive sequences? There is a lot of inter-individual variation in some of these sequences e.g. microsatelites/STRs

You could look at overlap of...
Forum: Bioinformatics 02-26-2013, 03:45 AM
Replies: 8
Views: 3,473
Posted By pmcget
I think you should take a look at some of the...

I think you should take a look at some of the extreme points in the plot in a genome browser and see if the raw data shows any evidence of weirdness - e.g.PCR artifacts - which would be visible as...
Forum: Bioinformatics 01-21-2013, 08:14 AM
Replies: 2
Views: 1,139
Posted By pmcget
You could have a mixture of real and artifactual...

You could have a mixture of real and artifactual MNPs - so a brute force filtering of them wouldn't be advisable.

Are you seeing a read-position bias to the adjacent SNPs? If you are then these...
Forum: RNA Sequencing 09-21-2010, 02:42 AM
Replies: 10
Views: 8,695
Posted By pmcget
Thanks for the suggestions - I didn't prepare the...

Thanks for the suggestions - I didn't prepare the samples myself.
Having spoken with the wetlab personnel I have found that the full RNA sample preparation protocol wasn't followed for some of the...
Forum: RNA Sequencing 08-19-2010, 06:28 AM
Replies: 10
Views: 8,695
Posted By pmcget
Problem with high background in some RNA-seq samples

I have been looking at some Illumina RNA-seq samples (84bp single read, bovine samples, 28 samples, 5 timepoints - developmental timecourse).
In 9 of the samples from this experiment we are seeing...
Forum: Service Providers 05-22-2009, 02:51 AM
Replies: 162
Views: 153,794
Posted By pmcget
University of Otago is in New Zealand - not...

University of Otago is in New Zealand - not Australia as listed.
Forum: Illumina/Solexa 06-04-2008, 06:25 AM
Replies: 20
Views: 8,233
Posted By pmcget
I think the higher number of NlaIII sites is due...

I think the higher number of NlaIII sites is due to need to avoid CpG dinucleotides in organisms where methylation of CpG's occurs.
NlaIII uses CATG sequence so CpG's are not are not a problem for...
Forum: Illumina/Solexa 04-30-2008, 09:09 AM
Replies: 18
Views: 7,406
Posted By pmcget
Here's a link to the Illumina DGE protocol...

Here's a link to the Illumina DGE protocol (http://arrayconsortium.tgen.org/np2/docs/PreparingSamplesforDigitalGeneExpression-TagProfilingwithNlaIII.pdf)
Forum: Sample Prep / Library Generation 04-16-2008, 09:35 AM
Replies: 18
Views: 12,623
Posted By pmcget
It's a bit difficult to tell based on such...

It's a bit difficult to tell based on such limited information. It could be either a problem with how you are using the aligner or a problem with the library prep or ....something else entirely
...
Forum: Sample Prep / Library Generation 03-28-2008, 08:29 AM
Replies: 29
Views: 25,061
Posted By pmcget
We've also been looking at this particular...

We've also been looking at this particular problem. At the moment we're trying to decide between the bioruptor (5-10k euros) and the covaris S2 (40-45k euros). The bioruptor seems to be capable of...
Forum: Events / Conferences 02-08-2008, 01:11 PM
Replies: 12
Views: 8,020
Posted By pmcget
Ben Blackburnes presentation from AGBT on...

Ben Blackburnes presentation from AGBT on slideshare.net (http://www.slideshare.net/guestb0fb1b/ssahapileup)
Forum: Polonator 02-08-2008, 05:34 AM
Replies: 42
Views: 34,004
Posted By pmcget
Hi Kevin, Congratulations on getting the...

Hi Kevin,
Congratulations on getting the Polonator into production! I think fans of open-source science will be rooting for the success of your machine.

I have a few specific questions that I was...
Forum: Events / Conferences 02-08-2008, 05:08 AM
Replies: 12
Views: 8,020
Posted By pmcget
...and Jonathan Eisen...

...and Jonathan Eisen (http://phylogenomics.blogspot.com/)
Forum: Events / Conferences 02-07-2008, 11:41 PM
Replies: 12
Views: 8,020
Posted By pmcget
I see that Anthony Fejes is live-blogging AGBT...

I see that Anthony Fejes is live-blogging AGBT (http://www.fejes.ca/blog.html)
Forum: Events / Conferences 02-07-2008, 09:27 AM
Replies: 12
Views: 8,020
Posted By pmcget
Live Blogging from Marco Island Next Gen Sequencing conference?

There appears to be a lot of excitement about the Marco Island conference this year? Are there any Seqanswers members attending who can update the rest of us?
Forum: 454 Pyrosequencing 01-25-2008, 09:38 AM
Replies: 61
Views: 73,919
Posted By pmcget
Does anyone know if the HD2 chips will be...

Does anyone know if the HD2 chips will be available for species other than human/mouse? Or if Nimblegen will make custom chips to order?
Forum: Academic/Non-Profit Jobs 01-22-2008, 11:52 AM
Replies: 0
Views: 3,078
Posted By pmcget
Bioinformatician wanted - Nextgen sequencing data management and analysis

Project Title: Bioinformatician (Research Fellow) for Next-generation
sequencing data management and analysis

Keyword descriptors: Bioinformatics, sequencing, pipeline, programming,
genome...
Showing results 1 to 25 of 28

 


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