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Forum: Bioinformatics 07-21-2016, 11:48 AM
Replies: 4
Views: 5,818
Posted By drea11
I'm attempting to extract barcodes from a set of...

I'm attempting to extract barcodes from a set of illumina miseq paired-end sequences and came across this post which seems to have the best description I have seen on the picard tools... tools. I...
Forum: Bioinformatics 04-08-2015, 09:50 AM
Replies: 1
Views: 1,125
Posted By drea11
Evaluate coverage of specific motifs

Is there a method out there that would allow me to determine whether a particular sequence motif (DNA) has adequate sequencing depth of coverage across a genome? What I am interested in seeing is...
Forum: Genomic Resequencing 02-02-2015, 11:45 AM
Replies: 1
Views: 3,465
Posted By drea11
WGS batch effects

Hi All,

I'm relatively new to whole genome sequencing, and have a background in 16S based typing of bacteria using NGS. I am collecting data on a set of closely related organism, using illumina,...
Forum: Bioinformatics 01-20-2015, 11:05 AM
Replies: 4
Views: 1,388
Posted By drea11
Thanks for the speedy reply. Could you perhaps...

Thanks for the speedy reply. Could you perhaps elaborate on your answer a bit? I'm not familiar with tabix, and the online documentation seems somewhat unspecific.
Forum: Bioinformatics 01-20-2015, 08:44 AM
Replies: 4
Views: 1,388
Posted By drea11
Extracting Regions of Zero Coverage

I am looking for a quick and simple way to identify regions of zero coverage in a sequencing set. My ultimate goal is to try and determine whether there might be genomic features which contribute to...
Forum: Bioinformatics 10-10-2014, 12:12 PM
Replies: 0
Views: 1,216
Posted By drea11
EdgeR - trim DGEList by data feature

Greetings!

I am using EdgeR to perform analysis on a large dataset. For some of my questions, I am interested in looking only at a subset of my data, based on a specific field in the dataset. Is...
Forum: Bioinformatics 08-18-2014, 06:20 AM
Replies: 3
Views: 1,250
Posted By drea11
Thank you!

Thank you!
Forum: General 08-15-2014, 11:17 AM
Replies: 2
Views: 1,226
Posted By drea11
Anyone know a good R course?

Greetings!

Does anyone know of any really amazing R-based statistics courses for users familiar with the language basics, but hoping to hone skills? Course would preferably be online and free/not...
Forum: Bioinformatics 08-15-2014, 11:11 AM
Replies: 3
Views: 1,250
Posted By drea11
EdgeR - default offset

Greetings R aficionados!

I was wondering whether anyone could tell me what the default offset is that is used in the glmFit function of EdgeR? Is it either the library size, or...
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