User: arno.guille
arno.guille • 400
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Posts by arno.guille
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... I suggest you to use phred phrap consed
http://www.phrap.org/phredphrapconsed.html
...
written 3.1 years ago by
arno.guille • 400
2
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817
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... 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 3.4 years ago by
arno.guille • 400
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... 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 3.4 years ago by
arno.guille • 400
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... 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 3.9 years ago by
arno.guille • 400
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... 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 3.9 years ago by
arno.guille • 400
0
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... it's better to merge fastq and then perform alignment
...
written 3.9 years ago by
arno.guille • 400
0
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... 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 4.1 years ago by
arno.guille • 400
6
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1.7k
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... 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 4.3 years ago by
arno.guille • 400
1
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1
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4.0k
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... 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 4.3 years ago by
arno.guille • 400
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