User: arno.guille

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arno.guille400
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Posts by arno.guille

<prev • 30 results • page 1 of 3 • next >
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Answer: A: Software to analyse mutations in sanger sequencing files
... I suggest you to use phred phrap consed http://www.phrap.org/phredphrapconsed.html ...
written 3.6 years ago by arno.guille400
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Answer: A: How to convert segmented aCGH probe-based to gene-based?
... Hello, Here is my solution : I use bedtools intersect to find overlaps between segdata output and genes coordinates (refseq from ucsc). bedtools intersect -a segData.bed -b genes.bed -loj > overlap.bed   Then with R res = read.table("overlap.bed",sep="\t",header=F) abs_max = tapply(res$ ...
written 3.9 years ago by arno.guille400
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Answer: A: Is there a database linking cell lines and mutations?
... Hi, http://www.cbioportal.org/ contains NCI-60 Cell Lines (NCI, Cancer Res. 2012) and Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012) dataset with mutation data. Hope this helps ...
written 3.9 years ago by arno.guille400
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Comment: C: BWA alignment using paired end reads from different lanes
... You probably get a segmentation fault due to lack of memory. Let's say you have 16 Gb of memory and 4 CPU. Each alignment process takes 6Gb in memory. If you run 4 alignments in the same time, you will need 4*6=24Gb. Unfortunately i have no solution, except to increase the memory space or run your a ...
written 4.4 years ago by arno.guille400
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Comment: C: BWA alignment using paired end reads from different lanes
... You're right it's faster, but in term of memory usage i'm not sure it is optimized. Of course it depends of your hardware specs. In my case, if i run 4 alignments on the same node i will get a nice segmentation fault.  ...
written 4.4 years ago by arno.guille400
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Comment: C: BWA alignment using paired end reads from different lanes
... exactly    ...
written 4.4 years ago by arno.guille400
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Comment: C: BWA alignment using paired end reads from different lanes
... it's better to merge fastq and then perform alignment ...
written 4.4 years ago by arno.guille400
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Answer: A: Unix or Linux which is better choice for genomic analysis?
... Linux is a Unix-Like operating system. There are many popular distributions based on Linux for example Red Hat, Fedora, openSUSE, Ubuntu, Linux Mint etc ... For a personal computer i suggest you Ubuntu or Linux Mint. ...
written 4.6 years ago by arno.guille400
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Answer: A: Can you automatically detect if reads are from Illumina or IonTorrent?
... To determine if the reads are from illumina or IonTorrent, i think the best solution is to look at the read names format in the fastq files. Illumina reads : @M02681:36:000000000-AAUMD:1:1101:17649:1746 1:N:0:1 @<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:& ...
written 4.8 years ago by arno.guille400
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Answer: A: hg19_cosmic_v54_120711.vcf for mutect analysis
... This file seems outdated and not available. I suggest you to download the latest cosmic vcf file from here : ftp://ngs.sanger.ac.uk/production/cosmic and to read this thread http://gatkforums.broadinstitute.org/discussion/2226/cosmic-and-dbsnp-files-for-mutect#latest ...
written 4.8 years ago by arno.guille400

Latest awards to arno.guille

Good Answer 4.7 years ago, created an answer that was upvoted at least 5 times. For A: Where To Download Pam50 Gene Set?
Scholar 4.7 years ago, created an answer that has been accepted. For A: Can you automatically detect if reads are from Illumina or IonTorrent?
Appreciated 4.8 years ago, created a post with more than 5 votes. For A: Where To Download Pam50 Gene Set?
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Where To Download Pam50 Gene Set?
Commentator 4.8 years ago, created a comment with at least 3 up-votes. For C: Hypergeometric Test On Gene Set
Good Answer 5.2 years ago, created an answer that was upvoted at least 5 times. For A: Where To Download Pam50 Gene Set?
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Where To Download Pam50 Gene Set?
Commentator 5.4 years ago, created a comment with at least 3 up-votes. For C: Hypergeometric Test On Gene Set
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Where To Download Pam50 Gene Set?

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