User: Aaron Statham
Aaron Statham • 1.1k
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- 1 year, 10 months ago
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Posts by Aaron Statham
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0
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answer
4.4k
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... Ever come across a Klinefelter?
...
written 3.2 years ago by
Aaron Statham • 1.1k
0
votes
3
answers
2.9k
views
3
answers
Comment:
C: Tool to unmark duplicates
... It should also be noted that "you can't do binf on a mac"
...
written 3.5 years ago by
Aaron Statham • 1.1k
0
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4
answers
4.4k
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4
answers
... How did that "other method in pre-publication" go?
...
written 3.8 years ago by
Aaron Statham • 1.1k
0
votes
2
answers
8.5k
views
2
answers
Comment:
C: Soft-Clipped Vs Unmapped?
... The mapping quality (5th field) is only 17, which equates to a 0.01995262% chance the mapping is incorrect which is quite high when you are mapping millions of reads.
...
written 4.2 years ago by
Aaron Statham • 1.1k
1
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3
answers
9.5k
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3
answers
... Hah at the moment I'm not paid to worry - there are always improvements to be made but a 0.85/0.95 correlation is good enough for me until someone does some serious benchmarking. ...
written 6.5 years ago by
Aaron Statham • 1.1k
0
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3
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9.5k
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3
answers
... Worst I've gotten between 450k and bisulfite seq is 0.85 and that was comparing primary cells (grown for a short time in culture) isolated between two different patients ie patient 1 on 450k, patient 2 on bis-seq. ...
written 6.5 years ago by
Aaron Statham • 1.1k
4
votes
3
answers
9.5k
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3
answers
... Below is my code for using minfi - I get a pearson correlation of 0.95 between beta values from a 450k array and whole genome bisulfite sequencing (cell line) so at least in my situation I don't know how much more there is to gain.
RG.raw <- read.450k.exp(base = slide.folder, targets = files.tabl ...
written 6.5 years ago by
Aaron Statham • 1.1k
2
votes
7
answers
6.7k
views
7
answers
... I did this a while ago, but never maintained it - you're free to cannibalise as much as you want/need! https://github.com/clark-lab-robot/Repitools-git/blob/master/pkg/Repitools/R/FastQC-class.R ...
written 6.6 years ago by
Aaron Statham • 1.1k
1
vote
2
answers
1.3k
views
2
answers
... I've used sense/antisense probe pairs on a Nimblegen custom array and when double stranded labelled material was hybed to them, the signals from the probe pairs indeed are highly correlated (pearson r>0.8). Unless you actually wish to interrogate each strand separately (therefore need single stra ...
written 6.8 years ago by
Aaron Statham • 1.1k
0
votes
3
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4.9k
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3
answers
... Ensembl has listed those three positions as separate genes - http://asia.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=3;q=OR4F29 - each with a single transcript of the exact same sequence. Personally I find RefSeq more... useful in this case ...
written 7.0 years ago by
Aaron Statham • 1.1k
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For How Can I Compare Enriched/Depleted Go Terms Between Genelists?
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For A: Is There An Alternative For Igb Which Can Display Normalized Rna-Seq Coverages?
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For A: Batch Viewing Of Ucsc Browser Graphic
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For A: What Are Some Sanity Checks That Should Be Performed On Ngs Data?
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For A: Generating Summary Statistics And Coverage Plots From Illumina Ga2 Data
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For A: What Are The Computing Requirements For Handling Illumina-Generated Reads?
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For A: What Is The Quickest Algorithm For Range Overlap?
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For Fastest Way Of Extracting Millions Of Short Sequences From The Human Genome
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For How Can I Compare Enriched/Depleted Go Terms Between Genelists?
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For Fastest Way Of Extracting Millions Of Short Sequences From The Human Genome
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For How Can I Compare Enriched/Depleted Go Terms Between Genelists?
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For A: Is There An Alternative For Igb Which Can Display Normalized Rna-Seq Coverages?
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created an answer that was upvoted at least 5 times.
For A: Batch Viewing Of Ucsc Browser Graphic
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4.5 years ago,
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For A: What Are Some Sanity Checks That Should Be Performed On Ngs Data?
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4.5 years ago,
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For A: What Are The Computing Requirements For Handling Illumina-Generated Reads?
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For A: What Is The Quickest Algorithm For Range Overlap?
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For Fastest Way Of Extracting Millions Of Short Sequences From The Human Genome
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For How Can I Compare Enriched/Depleted Go Terms Between Genelists?
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For C: What Is The Proper Control Sample For A Tumor Rna-Seq Experiment?
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For C: Tools For Chipseq Scale De Novo Motif Finding On Unaligned Sequences?
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4.5 years ago,
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For C: What Are The Computing Requirements For Handling Illumina-Generated Reads?
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