User: Louis Letourneau

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810
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Trusted
Location:
Montreal
Last seen:
5 years, 7 months ago
Joined:
10 years, 8 months ago
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Posts by Louis Letourneau

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Music Bmr Clustering...Why?
... It makes a lot of sens. But then the question is, how many clusters should you use? I guess you need to run the bmr part twice. One for each sample individually. Then inspect the bmr distribution, then rerun it with what you think is an acceptable cluster count. It would be nice to have MuSiC plot ...
written 7.7 years ago by Louis Letourneau810
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Music Bmr Clustering...Why?
... First off, I'm not an expert statistician, so bear with me please. I've been using MuSiC in my cancer analysis and I was wondering what was the point of clustering samples with similar BMRs together at the calc-bmr stage? The default is to cluster all BMRs together, I would have expected the defaul ...
music clustering cancer written 7.7 years ago by Louis Letourneau810 • updated 7.7 years ago by Cyriac Kandoth5.5k
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Error Hostname In Music
... I've been using Genome MuSic on an Ubuntu and CentOS6 machines without issues. I installed it on another server and I hit a problem that I traced back to Genome::Site. In the Begin block you identify the hostname and then try use $pkg. The problem is that the hostname has '-' in it. This breaks th ...
music written 8.0 years ago by Louis Letourneau810 • updated 8.0 years ago by nnutter210
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Answer: A: Music Source Code
... The devs put the perl section up in CPAN so I was able to install it on centos 6 machines using perl -MCPAN for the perl parts and I compiled + installed joinx and calcRoiCovg separately. I only had to add joinx, calcRoiCovg and genome (in the your perl cpan installation repository) to PATH. As o ...
written 8.0 years ago by Louis Letourneau810
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Answer: A: Comparing Multiple Genome Assemblies With Reference
... nucmer + show-coord from the MUMur (http://mummer.sourceforge.net/) is very useful to do this. I've used this many, many times. Mauve also is a very good tool to show regions that overlap between the assemblies, although I have had problems with mauve with big genomes. Your mileage may vary. http:// ...
written 9.1 years ago by Louis Letourneau810
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Comment: C: Disk I/O Bound Genome Analysis Application
... You usually want normal/standard benchmarks like SPEC, bonnie and the like, but it's always good to do a synthetic, almost real-world test to see if the hardware supports what you really do day-in day-out. ...
written 9.2 years ago by Louis Letourneau810
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Comment: C: How To Distinguish Heterozygotes And Homozygotes From Variants In Vcf Format?
... That answers that the GT field is probably the best one to use, but it doesn't answer why the different "tests" give five different values. There's a 5k difference between tests, that's a lot! ...
written 9.2 years ago by Louis Letourneau810
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Answer: A: Disk I/O Bound Genome Analysis Application
... I had to write a similar benchmark. I wrote a random fastq generator that follows the illumina hiseq error rate (kind of). Then I ran the first step of any pipeline, clipping adapters + read quality trimming. It seems to do the job of stressing IO pretty nicely. The rest of the pipeline, Alignment, ...
written 9.2 years ago by Louis Letourneau810
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Comment: C: What Is The Most Memory-Efficient De Novo Assembler?
... How did you go about extracting reads from the jellyfish output? Say you would want to ignore kmers with counts 1-6? I wrote something myself buts it is very slow. It's a shame helly loses read info from the kmers. ...
written 9.3 years ago by Louis Letourneau810
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Answer: A: Improving Performance Of Picard For Markduplicates
... The setting, -XX:ParallelGCThreads, is just for garbage collection. It won't really affect MArkDuplicates unless MarkDups hits it's top memory usage (The -Xmx setting). As for -XX:-UseGCOverheadLimit it will just make MarkDups die faster if the Xmx wasn't set high enough. They are all java hotspot s ...
written 9.4 years ago by Louis Letourneau810

Latest awards to Louis Letourneau

Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: Comparing Multiple Genome Assemblies With Reference
Appreciated 6.8 years ago, created a post with more than 5 votes. For A: In Silico Genome Digestion ?
Appreciated 6.8 years ago, created a post with more than 5 votes. For A: Determining Which New Snps In 1000G Data Result In Coding Changes
Appreciated 6.8 years ago, created a post with more than 5 votes. For A: Convert Illumina Reads To Sanger Score
Appreciated 6.8 years ago, created a post with more than 5 votes. For A: What Methods Do You Use For In/Del/Snp Calling?
Appreciated 6.8 years ago, created a post with more than 5 votes. For A: Samtools + Picard Markduplicates
Good Answer 6.8 years ago, created an answer that was upvoted at least 5 times. For A: Determining Which New Snps In 1000G Data Result In Coding Changes
Good Answer 6.8 years ago, created an answer that was upvoted at least 5 times. For A: Convert Illumina Reads To Sanger Score
Good Answer 6.8 years ago, created an answer that was upvoted at least 5 times. For A: What Methods Do You Use For In/Del/Snp Calling?
Good Answer 6.8 years ago, created an answer that was upvoted at least 5 times. For A: Samtools + Picard Markduplicates
Supporter 6.8 years ago, voted at least 25 times.
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Comparing Multiple Genome Assemblies With Reference
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Whole-Exome Data Cleanup / Filtering
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Stand Alone Otu Generation Program (Ngs)
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Human Exome Capture Library Coordinates Download
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: How Can I Convert Bam/Sam To Wiggle
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: 454 And Opgen Assembly
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: In Silico Genome Digestion ?
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Determining Which New Snps In 1000G Data Result In Coding Changes
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: How To Check If The Iupac Snp Code Changes Translation ?
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Artemis, Apollo Or Anything For Genome Annotation Editing With Next Gen Sequenc
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Content Management Systems For Bioinformatics Websites
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Convert Illumina Reads To Sanger Score
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: What Methods Do You Use For In/Del/Snp Calling?
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Samtools + Picard Markduplicates

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