Forum: Academic/Non-Profit Jobs
05-26-2015, 04:58 AM
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Replies: 0
Views: 748
Computational biologist, programming oriented
The Center of Translational Genomics and Bioinformatics (CTGB) is seeking a motivated individual to reinforce the development team responsible for original analytical tools and platforms.
The role...
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Forum: Academic/Non-Profit Jobs
05-26-2015, 04:48 AM
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Replies: 0
Views: 692
Computational biologist, analysis oriented
The Center of Translational Genomics and Bioinformatics (CTGB) is seeking a profile to reinforce the core team responsible for analysis of omics data generated by the Genomics Unit.
The role will...
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Forum: Bioinformatics
10-31-2013, 03:48 AM
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Replies: 2
Views: 2,197
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Forum: Bioinformatics
05-30-2013, 02:17 AM
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Replies: 2
Views: 1,481
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Forum: Bioinformatics
02-12-2013, 02:42 PM
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Replies: 4
Views: 2,619
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Forum: Bioinformatics
02-01-2013, 02:12 AM
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Replies: 4
Views: 4,894
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Forum: Bioinformatics
01-30-2013, 03:00 AM
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Replies: 4
Views: 4,894
Looking for best strategy to realign BAM files
Hi all, I was given a set of BAM files (100 Gb each) that I would like to realign using bwa. Problem is, I would like to have the best speed for doing this.
At the moment start from chunked fastq...
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Forum: Bioinformatics
11-27-2012, 12:29 AM
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Replies: 5
Views: 4,089
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Forum: Bioinformatics
11-21-2012, 08:50 AM
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Replies: 4
Views: 5,983
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Forum: General
08-31-2012, 12:58 AM
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Replies: 1
Views: 2,920
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Forum: Bioinformatics
08-31-2012, 12:57 AM
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Replies: 1
Views: 1,957
cuffdiff and limma, puzzled by the differences
Hi all, I've been using cuffdiff for a long time but recently I've given limma (voom) a try for RNA-seq data and compared the results.
The experiment is quite simple, a triplicate in a treatment vs...
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Forum: Bioinformatics
07-03-2012, 03:05 AM
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Replies: 1
Views: 8,233
AFAIK htseq-count supports several ways to...
AFAIK htseq-count supports several ways to perform the intersection, hence you may want to post the actual command lines with all parameters used. multiBamCov supports flag filtering.
What do you...
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Forum: Bioinformatics
07-03-2012, 02:57 AM
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Replies: 7
Views: 2,251
Is that the IndelRealigner? I found the same...
Is that the IndelRealigner? I found the same problem with TableRecalibration, but that happens because GATK retains old quality scores for each read. Solved with "--doNotWriteOriginalQuals" options.
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Forum: Bioinformatics
06-13-2012, 05:40 AM
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Replies: 5
Views: 2,732
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Forum: Bioinformatics
06-13-2012, 03:54 AM
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Replies: 3
Views: 2,064
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Forum: Bioinformatics
05-10-2012, 08:48 AM
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Replies: 2
Views: 2,642
Try this...
Try this http://genomebiology.com/content/pdf/gb-2012-13-3-r16.pdf.
Anyway, macs2 has options to scale one sample to the other if the number of reads is larger
d
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Forum: Bioinformatics
05-02-2012, 02:56 AM
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Replies: 5
Views: 5,182
bamtools...
bamtools (https://github.com/pezmaster31/bamtools) can filter on sequence tags:
$ bamtools filter -h
Description: filters BAM file(s).
Usage: bamtools filter [-in <filename> -in <filename>...
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Forum: Bioinformatics
04-21-2012, 06:13 AM
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Replies: 2
Views: 4,441
Hello there
If you have sharp signals...
Hello there
If you have sharp signals in your input you should find them in IP too. BTW, MNase input should be naked DNA, which is not the same input as in general ChIP-seq data
If you...
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Forum: Bioinformatics
03-29-2012, 02:17 AM
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Replies: 3
Views: 1,965
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Forum: Academic/Non-Profit Jobs
02-16-2012, 01:30 AM
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Replies: 0
Views: 2,041
Data analyst
Job Title:
Data Analysts
Description:
The Center for Translational Genomics and Bioinformatics was founded at San Raffaele in 2010 and in 2011 significant investments were made to setup...
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Forum: Bioinformatics
01-20-2012, 05:47 AM
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Replies: 2
Views: 3,074
Good point, thanks!
Besides... I've realized I...
Good point, thanks!
Besides... I've realized I must know what trimming process has been applied. If 5' trimming, the inner size remains the same, if 3' trimming I will try to evaluate mean/stddev
...
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Forum: Bioinformatics
01-20-2012, 04:44 AM
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Replies: 2
Views: 3,074
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Forum: Bioinformatics
01-18-2012, 01:54 AM
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Replies: 7
Views: 25,158
Hi there, you can use bx-python...
Hi there, you can use bx-python (https://bitbucket.org/james_taylor/bx-python/wiki/Home) to read BigFile (i.e. bigWig and bigBed). if foo.bigwig is your file you can
import bx.bbi.bigwig_file
bwh...
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Forum: Bioinformatics
01-17-2012, 02:46 PM
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Replies: 19
Views: 5,869
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Forum: Bioinformatics
01-17-2012, 02:09 PM
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Replies: 19
Views: 5,869
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