User: Aaron Statham

gravatar for Aaron Statham
Aaron Statham1.1k
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Australia
Last seen:
1 year, 10 months ago
Joined:
8 years, 4 months ago
Email:
a**************@gmail.com

Posts by Aaron Statham

<prev • 58 results • page 1 of 6 • next >
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Comment: C: how to identify a sequencing sample's gender
... Ever come across a Klinefelter? ...
written 3.2 years ago by Aaron Statham1.1k
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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 Statham1.1k
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Comment: C: P Value Or Statistical Significance Of Real Peak Compared To Random Peak Overlap
... How did that "other method in pre-publication" go? ...
written 3.8 years ago by Aaron Statham1.1k
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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 Statham1.1k
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Comment: C: Your Thoughts On A "Standard" Pipeline To Process Illumina 450K Data
... 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 Statham1.1k
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Comment: C: Your Thoughts On A "Standard" Pipeline To Process Illumina 450K Data
... 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 Statham1.1k
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Answer: A: Your Thoughts On A "Standard" Pipeline To Process Illumina 450K Data
... 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 Statham1.1k
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Comment: C: Fastqc Html Report To Pdf (With A Script)
... 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 Statham1.1k
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Answer: A: What Are The Downsides Of Replicated Spots On A Microarray?
... 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 Statham1.1k
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Comment: C: Why Some Refseq Genes Have Several Transcripts With Different Strands?
... 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 Statham1.1k

Latest awards to Aaron Statham

Great Question 3.2 years ago, created a question with more than 5,000 views. For How Can I Compare Enriched/Depleted Go Terms Between Genelists?
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Batch Viewing Of Ucsc Browser Graphic
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: What Are Some Sanity Checks That Should Be Performed On Ngs Data?
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Generating Summary Statistics And Coverage Plots From Illumina Ga2 Data
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: What Are The Computing Requirements For Handling Illumina-Generated Reads?
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Bwa: Number Of Threads
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: What Is The Quickest Algorithm For Range Overlap?
Appreciated 4.5 years ago, created a post with more than 5 votes. For Fastest Way Of Extracting Millions Of Short Sequences From The Human Genome
Appreciated 4.5 years ago, created a post with more than 5 votes. For How Can I Compare Enriched/Depleted Go Terms Between Genelists?
Good Question 4.5 years ago, asked a question that was upvoted at least 5 times. For Fastest Way Of Extracting Millions Of Short Sequences From The Human Genome
Good Question 4.5 years ago, asked a question that was upvoted at least 5 times. For How Can I Compare Enriched/Depleted Go Terms Between Genelists?
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Is There An Alternative For Igb Which Can Display Normalized Rna-Seq Coverages?
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Batch Viewing Of Ucsc Browser Graphic
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: What Are Some Sanity Checks That Should Be Performed On Ngs Data?
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: What Are The Computing Requirements For Handling Illumina-Generated Reads?
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Quickest Algorithm For Range Overlap?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Fastest Way Of Extracting Millions Of Short Sequences From The Human Genome
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How Can I Compare Enriched/Depleted Go Terms Between Genelists?
Guru 4.5 years ago, received more than 100 upvotes.
Voter 4.5 years ago, voted more than 100 times.
Supporter 4.5 years ago, voted at least 25 times.
Commentator 4.5 years ago, created a comment with at least 3 up-votes. For C: What Is The Proper Control Sample For A Tumor Rna-Seq Experiment?
Commentator 4.5 years ago, created a comment with at least 3 up-votes. For C: Tools For Chipseq Scale De Novo Motif Finding On Unaligned Sequences?
Commentator 4.5 years ago, created a comment with at least 3 up-votes. For C: What Are The Computing Requirements For Handling Illumina-Generated Reads?

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