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Forum: Illumina/Solexa 01-07-2018, 10:09 PM
Replies: 1
Views: 921
Posted By hr3y
Lightbulb EstimateLibraryComplexity

Possibly running This tool (https://broadinstitute.github.io/picard/command-line-overview.html#EstimateLibraryComplexity) and make decisions from there?

:eek:
Forum: Illumina/Solexa 01-07-2018, 09:01 PM
Replies: 1
Views: 921
Posted By hr3y
Question Find out if you have amplicon reads.

Is there really no way (program, tool) to tell if your BAM files have amplicon reads?

How is everyone doing it? determining a priori and using different analysis pipelines? or is this done by...
Forum: Bioinformatics 06-29-2017, 01:31 PM
Replies: 0
Views: 940
Posted By hr3y
Question GATK HaplotypeCaller READS?

Hi everyone, I was wondering if anyone knows exactly how does GATK HaplotypeCaller treat unmapped reads.

The thing is, first GATK defines <<active regions>> in which it will operate, after this,...
Forum: Illumina/Solexa 05-30-2017, 12:12 PM
Replies: 26
Views: 10,946
Posted By hr3y
Yes... I guess we would have to take a look at...

Yes... I guess we would have to take a look at the code to figure out wth with the permissions. I did something lazy which is just an importer that hard links to the files and changes permissions in...
Forum: Illumina/Solexa 05-29-2017, 10:01 AM
Replies: 26
Views: 10,946
Posted By hr3y
Unhappy basemount is weird.

Hi everyone, I was wondering if anyone has experience with mounting their BaseSpace account and regularly using it (reading, copying from it, etc). I was just trying to change the permissions of the...
Forum: Bioinformatics 05-08-2017, 11:12 AM
Replies: 1
Views: 1,027
Posted By hr3y
ABRA-marked duplicates

Hello,

I was wondering if anyone knows what does ABRA - Assembly Based ReAligner (https://github.com/mozack/abra) do with marked PCR duplicates?

from reading the thread I saw the...
Forum: Introductions 05-08-2017, 10:57 AM
Replies: 0
Views: 785
Posted By hr3y
Smile Hello World, I am interested in gene expression...

Hello World, I am interested in gene expression regulation + evolution, although currently I am working on genetic variants analysis from exome panels (soon to be whole exome, I think).
Anyhow,...
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