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Forum: Academic/Non-Profit Jobs 05-26-2015, 03:58 AM
Replies: 0
Views: 463
Posted By dawe
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...
Forum: Academic/Non-Profit Jobs 05-26-2015, 03:48 AM
Replies: 0
Views: 422
Posted By dawe
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...
Forum: Bioinformatics 10-31-2013, 02:48 AM
Replies: 2
Views: 1,641
Posted By dawe
You can use wigCorrelate for bedgraph, wig and...

You can use wigCorrelate for bedgraph, wig and bigwig files. It does pearson correlation on intervals that have non-zero value on both the datasets.
Forum: Bioinformatics 05-30-2013, 01:17 AM
Replies: 2
Views: 1,085
Posted By dawe
You may deal with aptamer sequences using only...

You may deal with aptamer sequences using only bash utilities with grep, awk, sort and uniq.
First of all you have to put all sequences (one per line) in a file, then

$ sort file | uniq -c |...
Forum: Bioinformatics 02-12-2013, 01:42 PM
Replies: 4
Views: 1,820
Posted By dawe
I had the same issue and wrote to the developer....

I had the same issue and wrote to the developer. He said he would have checked that but there have been no updates since then.
I've tried to run CONTRA with python debugger, I remember there was a...
Forum: Bioinformatics 02-01-2013, 01:12 AM
Replies: 4
Views: 3,615
Posted By dawe
These are PE data. I've started a bwa realignment...

These are PE data. I've started a bwa realignment directly from BAM, using bwa threads in alignment. sampe step will take ages, though...
thanks

d
Forum: Bioinformatics 01-30-2013, 02:00 AM
Replies: 4
Views: 3,615
Posted By dawe
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...
Forum: Bioinformatics 11-26-2012, 11:29 PM
Replies: 5
Views: 3,337
Posted By dawe
You can try zgrep -hv 'track' *.wig.gz |...

You can try

zgrep -hv 'track' *.wig.gz | wigToBigWig -clip stdin chromsizes.tab output.bigwig
Forum: Bioinformatics 11-21-2012, 07:50 AM
Replies: 4
Views: 2,179
Posted By dawe
You can try genemania, either the web interface ...

You can try genemania, either the web interface (http://www.genemania.org)or (better) the Cytoscape plugin

HTH
Forum: General 08-30-2012, 11:58 PM
Replies: 1
Views: 2,203
Posted By dawe
According to limma authors, you should not use...

According to limma authors, you should not use limma with RPKM, as it will estimate CPM from raw counts...
Forum: Bioinformatics 08-30-2012, 11:57 PM
Replies: 1
Views: 1,410
Posted By dawe
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...
Forum: Bioinformatics 07-03-2012, 02:05 AM
Replies: 1
Views: 7,226
Posted By dawe
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...
Forum: Bioinformatics 07-03-2012, 01:57 AM
Replies: 7
Views: 1,779
Posted By dawe
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.
Forum: Bioinformatics 06-13-2012, 04:40 AM
Replies: 5
Views: 2,143
Posted By dawe
Take a look to the latest SnpSift developments....

Take a look to the latest SnpSift developments. It does not perform what you need directly, but it should be easy to perform what you want once you created a single VCF with multiple samples
Forum: Bioinformatics 06-13-2012, 02:54 AM
Replies: 3
Views: 1,465
Posted By dawe
Hi there, we are working on it also. The main...

Hi there, we are working on it also. The main problem we have is that we cannot achieve a reasonable level of parallelism (i.e. we cannot split GATK bam Walkers to run by chromosome)
Forum: Bioinformatics 05-10-2012, 07:48 AM
Replies: 2
Views: 2,032
Posted By dawe
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
Forum: Bioinformatics 05-02-2012, 01:56 AM
Replies: 5
Views: 3,436
Posted By dawe
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>...
Forum: Bioinformatics 04-21-2012, 05:13 AM
Replies: 2
Views: 3,306
Posted By dawe
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...
Forum: Bioinformatics 03-29-2012, 01:17 AM
Replies: 3
Views: 1,435
Posted By dawe
Whoa! That's pretty interesting. I'm at Brabaham...

Whoa! That's pretty interesting. I'm at Brabaham for EagleGenomics Symposium today... do you think we can meet and chat about it?

d
Forum: Academic/Non-Profit Jobs 02-16-2012, 12:30 AM
Replies: 0
Views: 1,730
Posted By dawe
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...
Forum: Bioinformatics 01-20-2012, 04:47 AM
Replies: 2
Views: 2,375
Posted By dawe
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
...
Forum: Bioinformatics 01-20-2012, 03:44 AM
Replies: 2
Views: 2,375
Posted By dawe
tophat, --mate-inner-dist and variable length reads

Hi there, I have variable length RNA-seq reads ranging from 42 to 76 bp (I guess because of a trimming process). Since I have to specify --mate-inner-dist parameter, which would be the correct value?...
Forum: Bioinformatics 01-18-2012, 12:54 AM
Replies: 7
Views: 16,795
Posted By dawe
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...
Forum: Bioinformatics 01-17-2012, 01:46 PM
Replies: 19
Views: 4,725
Posted By dawe
I'm using fastq-join and fastq-mcf. The first for...

I'm using fastq-join and fastq-mcf. The first for overlapping paired end reads, the second to de-multiplex NuGEN RNA-seq libraries.
I'm trying to get some more doc (the developer is very active...)
Forum: Bioinformatics 01-17-2012, 01:09 PM
Replies: 19
Views: 4,725
Posted By dawe
ea-utils (http://code.google.com/p/ea-utils/) is...

ea-utils (http://code.google.com/p/ea-utils/) is really fast, unfortunately lacks proper documentation
Showing results 1 to 25 of 258

 


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