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Forum: Clinical Sequencing 06-20-2018, 06:25 AM
Replies: 0
Views: 965
Posted By puggie
Allele frequency discrepancies in Illumina data?

Dear forum members,

We are using the TST-15 Illumina panel and occasionally detect variant frequencies that appear not to be of biological relevance. I.e. frequencies in the range of 60-90%. A...
Forum: Bioinformatics 12-10-2014, 01:08 PM
Replies: 3
Views: 704
Posted By puggie
Ideas for graphing data?

I have developed a method that identifies some genomic features and does so tissue-specifically. Now I would like to make some visual representation of this. E.g in one type of tissue I get lets say...
Forum: Literature Watch 12-10-2014, 12:57 PM
Replies: 0
Views: 1,421
Posted By puggie
Forum: Bioinformatics 03-05-2014, 09:04 AM
Replies: 4
Views: 1,079
Posted By puggie
I have one more question I hope some of you can...

I have one more question I hope some of you can answer.

E.g. if I compare Group A and Group B and the difference is X, then i compare Group A and C, the difference is Y, and then I compare Group B...
Forum: Bioinformatics 02-27-2014, 12:25 PM
Replies: 4
Views: 1,079
Posted By puggie
Hej dpryan, And thanks for your answer, yes...

Hej dpryan,

And thanks for your answer, yes the randomized regions are "close to" the original ChIP dataset in terms of "overall" location, and exclusion of unmappable (random) genome sequence,...
Forum: Bioinformatics 02-27-2014, 11:38 AM
Replies: 4
Views: 1,079
Posted By puggie
Questions: Simulation statistics (genomic overlaps)

Dear forum,
I have some questions that are likely very basic for many of you but I am hoping for answers anyways.

Im doing some overlap (intersection) analysis between a dataset of genomic...
Forum: RNA Sequencing 02-25-2014, 09:32 AM
Replies: 5
Views: 2,438
Posted By puggie
Well, I think the quickest test to assess if they...

Well, I think the quickest test to assess if they are directional and how forward to reverse are handled in the librarires, you could map to a couple of genes and have a look in e.g. IGV to see if it...
Forum: RNA Sequencing 02-19-2014, 04:03 PM
Replies: 3
Views: 2,971
Posted By puggie
700 samples sounds like a lot, guess you'll be...

700 samples sounds like a lot, guess you'll be pooling many samples on the lanes unless you have good resources, one lane would give something around 400 million reads. Are you looking for...
Forum: RNA Sequencing 02-19-2014, 03:56 PM
Replies: 3
Views: 2,530
Posted By puggie
You could use e.g. Cufflinks or DEseq to...

You could use e.g. Cufflinks or DEseq to calculate the library depths, at least that would provide you a scaling factor for inter-library comparisons and normalization. I think the "sequencing depth"...
Forum: RNA Sequencing 02-19-2014, 03:48 PM
Replies: 4
Views: 5,362
Posted By puggie
I'm glad it work out for you :) Depending on what...

I'm glad it work out for you :) Depending on what you are looking for depth is something to consider.

Out of curiosity how did you sequence, i.e. reads/sample?
Forum: RNA Sequencing 02-19-2014, 03:26 PM
Replies: 5
Views: 2,438
Posted By puggie
What protocol did you use for library...

What protocol did you use for library preparation? Normally for ScriptSeq Illumina libraries, the forward reads would correspond to the DNA coding strand while the reverse reads would be reverse...
Forum: Site Feedback/Suggestions 02-19-2014, 03:22 PM
Replies: 0
Views: 25,543
Posted By puggie
Request for general threads on Biology and Statistics

I find this forum very informative. However, I would appreciate (as we are probably many biologists here) that there would be subfora dedicated to general questions regarding biology and also the...
Forum: RNA Sequencing 02-10-2014, 02:34 PM
Replies: 1
Views: 1,507
Posted By puggie
cummeRbund JS Distances (Jensen–Shannon divergence)

Has anyone used the cummerRbund bioconductor package on RNA-seq data?

How does one interpret the data?

I have 6 samples no replicates, of 2 different tissues. cummeRbund shows clear clustering...
Forum: Bioinformatics 10-24-2013, 11:20 AM
Replies: 7
Views: 5,404
Posted By puggie
I think there is a technical factor to take into...

I think there is a technical factor to take into consideration. Although libraries are strand-specific (scriptseq), I believe there is some contamination to this, dna, wrong direction etc... At...
Forum: Sample Prep / Library Generation 10-10-2013, 12:34 PM
Replies: 0
Views: 1,683
Posted By puggie
Validated ChIP qPCR Primer Database?

I'm looking for a resource for fast qPCR validation of mouse ChIP-seq experiments, i.e. primer sequences, to save time. Does something like that exist, at least for well-established IPs such as...
Forum: Bioinformatics 10-09-2013, 05:47 AM
Replies: 8
Views: 2,222
Posted By puggie
Jeremy, do you remember how large your target...

Jeremy, do you remember how large your target region was as percent of total and read length
Forum: Bioinformatics 10-08-2013, 12:31 PM
Replies: 8
Views: 2,222
Posted By puggie
Ok thx for the suggestion I will have a look at...

Ok thx for the suggestion I will have a look at the bedtools possibilities. Also I am aware that mapping all reads to a few specified regions may result in "false" alignments. I believe this can be...
Forum: Bioinformatics 10-08-2013, 11:15 AM
Replies: 8
Views: 2,222
Posted By puggie
Perhaps I should explain more, I want to map to...

Perhaps I should explain more, I want to map to specific regions at first hand to decrease computation time, still I want the resulting alignment files to be compatible with the reference genome...
Forum: Bioinformatics 10-08-2013, 07:54 AM
Replies: 8
Views: 2,222
Posted By puggie
Mapping to specified parts of a genome?

Is it possible to map reads to specified parts of the genome using BWA or Bowtie or other tools without directly customizing the reference genome or map to single chromosomes?

E.g. if one wants to...
Forum: Epigenetics 10-08-2013, 07:42 AM
Replies: 0
Views: 1,570
Posted By puggie
ChIP-seq Analysis treated vs. non-treated vs. input controls?

I am currently planning to do ChIP-seq and have therefore been mapping some available data from ENCODE to gain some experience.

Common programs such as MACS can accomodate two input files i.e....
Forum: Sample Prep / Library Generation 10-01-2013, 06:31 AM
Replies: 0
Views: 867
Posted By puggie
ChIA-PET commercial solutions?

We are currently looking into performing ChIA-PET experiments, however we find it difficult to find comercial kits for for this kind of experiment, i.e. including all neccesary materials except AB....
Forum: General 09-11-2013, 09:36 AM
Replies: 4
Views: 3,058
Posted By puggie
If you use UCSC GB you can export as pdf for...

If you use UCSC GB you can export as pdf for Adobe Illustrator, and generate high-res pictures.
Forum: General 09-11-2013, 09:34 AM
Replies: 1
Views: 1,315
Posted By puggie
Publishing large seq. data, repositories and date for data availability?

Dear forum,

We are currently in the process of submitting a manuscript, but do not wish to make the raw sequencing data available publically prior to acceptance. Also, where can we upload these...
Forum: Bioinformatics 09-02-2013, 02:47 PM
Replies: 4
Views: 2,720
Posted By puggie
thanks for your reply I will look into that. I ...

thanks for your reply I will look into that. I should also mention that the table I showed above is errornous.

It should be like
900 200
300 1000

So e.g. I have 1200 features, 900 hundred...
Forum: Bioinformatics 09-02-2013, 10:52 AM
Replies: 4
Views: 2,720
Posted By puggie
Proper statistical test for high-throughput data correlations?

Dear Forum Members,
I have been analyzing correlations between ENCODE data and my own data. Specifically I have been looking at overlapping (or intersecting) coordinates between data sets to assess...
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