User: arno.guille
arno.guille • 400
- Reputation:
- 400
- Status:
- Trusted
- Location:
- France
- Last seen:
- 4 years, 5 months ago
- Joined:
- 8 years, 3 months ago
- Email:
- a**********@gmail.com
about me
Posts by arno.guille
<prev
• 30 results •
page 1 of 3 •
next >
1
vote
3
answers
3.5k
views
3
answers
... I suggest you to use phred phrap consed
http://www.phrap.org/phredphrapconsed.html
...
written 5.0 years ago by
arno.guille • 400
2
votes
1
answer
1.1k
views
1
answers
... 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( ...
written 5.3 years ago by
arno.guille • 400
• updated
14 months ago by
_r_am ♦ 32k
2
votes
1
answer
6.4k
views
1
answers
... 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 5.3 years ago by
arno.guille • 400
0
votes
3
answers
6.1k
views
3
answers
... 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 5.8 years ago by
arno.guille • 400
0
votes
3
answers
6.1k
views
3
answers
... 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 5.8 years ago by
arno.guille • 400
0
votes
3
answers
6.1k
views
3
answers
... it's better to merge fastq and then perform alignment
...
written 5.8 years ago by
arno.guille • 400
0
votes
3
answers
2.8k
views
3
answers
... 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 6.0 years ago by
arno.guille • 400
6
votes
1
answer
2.2k
views
1
answers
... 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 6.2 years ago by
arno.guille • 400
1
vote
1
answer
4.8k
views
1
answers
... 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 6.2 years ago by
arno.guille • 400
Latest awards to arno.guille
Good Answer
6.1 years ago,
created an answer that was upvoted at least 5 times.
For A: Where To Download Pam50 Gene Set?
Scholar
6.1 years ago,
created an answer that has been accepted.
For A: Can you automatically detect if reads are from Illumina or IonTorrent?
Appreciated
6.2 years ago,
created a post with more than 5 votes.
For A: Where To Download Pam50 Gene Set?
Teacher
6.2 years ago,
created an answer with at least 3 up-votes.
For A: Where To Download Pam50 Gene Set?
Commentator
6.2 years ago,
created a comment with at least 3 up-votes.
For C: Hypergeometric Test On Gene Set
Good Answer
6.6 years ago,
created an answer that was upvoted at least 5 times.
For A: Where To Download Pam50 Gene Set?
Appreciated
6.8 years ago,
created a post with more than 5 votes.
For A: Where To Download Pam50 Gene Set?
Commentator
6.8 years ago,
created a comment with at least 3 up-votes.
For C: Hypergeometric Test On Gene Set
Teacher
6.8 years ago,
created an answer with at least 3 up-votes.
For A: Where To Download Pam50 Gene Set?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1003 users visited in the last hour