User: Michael.James.Clark

Reputation:
560
Status:
New User
Location:
Palo Alto
Website:
http://breakway.sf.net
Last seen:
6 years, 11 months ago
Joined:
9 years, 5 months ago
Email:
m******************@gmail.com

Geneticist & bioinformatician at Stanford University. Whole genomes, exomes and RNAseq. Author of Breakway (a tool for structural variation detection).

Posts by Michael.James.Clark

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Picking A Programming Language And Where To Begin
... Inspiring! From now on, I'm writing all my programs in なでしこ! ;) ...
written 8.8 years ago by Michael.James.Clark560
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... That's correct, panos. This simple solution is only if every base is covered at least once because samtools pileup doesn't report bases with zero coverage. Thanks for pointing that out! ...
written 8.9 years ago by Michael.James.Clark560
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Comment: C: What Is Ad (Allelic Depth) In 1000Genomes Vcf?
... So, to clarify: DP is equal to the number of reads used for calling the variant AD numbers are the total number of reads with each allele (including reads not used for calling due to low quality or whatever). Seems un-intuitive to me, but I'll take it. ...
written 9.3 years ago by Michael.James.Clark560
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Answer: A: Online Bioinformatics Resources
... As a resource, the SEQanswers forum is very valuable for people in the sequencing space. The Bioinformatics forum there is often one of the most updated sources of information regarding sequence analysis techniques. ...
written 9.3 years ago by Michael.James.Clark560
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Comment: C: Difference Between Gwa And Gwls
... This is a good answer. I admit I haven't heard of "GWLS" either. The way I've generally taught students to tell between linkage and association is the presence or absence of a pedigree. I would imagine a "GWLS" would simply be sequencing the whole genome of related individuals and assessing linkage ...
written 9.3 years ago by Michael.James.Clark560
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Comment: C: 1000 Genomes Indel/Snps File
... Seems redundant with my answer. ...
written 9.3 years ago by Michael.James.Clark560
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Answer: A: How Do You Test The Global Null Hypothesis In Expression Analysis?
... Typically we use a clustering approach to estimate how closely related expression profiles are on a global scale. Hierarchical and k-means clustering are both commonly used. The similarity of the clusters can then be calculated. So yes, it is indeed performing multiple independent tests and aggregat ...
written 9.3 years ago by Michael.James.Clark560
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Answer: A: 1000 Genomes Indel/Snps File
... Have you checked [the 1000 Genomes site](http://www.1000genomes.org/)? They had a major release of all the merged phase 1 data in November 2010 which you can obtain VCF files from [the ftp link here](ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/2010_11/). ...
written 9.3 years ago by Michael.James.Clark560 • updated 9 months ago by RamRS27k
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Comment: C: Retrieving Best N Local Alignments
... Ah sorry, I guess I misunderstood. Looks like exonerate might be just what you need then! Good luck! ...
written 9.4 years ago by Michael.James.Clark560
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Answer: A: Tools To Calculate Average Coverage For A Bam File?
... Here's a very simple perl script I wrote that does exactly this that you're free to use: ($num,$den)=(0,0); while ($cov=) { $num=$num+$cov; $den++; } $cov=$num/$den; print "Mean Coverage = $cov\n"; Just pipe [samtools](http://samtools.sourceforge.net/) pileup to ...
written 9.4 years ago by Michael.James.Clark560 • updated 22 months ago by RamRS27k

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