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Forum: Bioinformatics 02-25-2016, 04:35 AM
Replies: 4
Views: 2,180
Posted By Fabien Campagne
I realize you are likely done with your thesis,...

I realize you are likely done with your thesis, so this information is for those who may stumble upon this thread. I would suggest to take a look at the latest development: NextflowWorkbench. Here's...
Forum: Bioinformatics 02-25-2016, 04:14 AM
Replies: 0
Views: 659
Posted By Fabien Campagne
Workflow/pipeline system for beginners and experts

The latest preprint from our lab describes NexflowWorkbench:

NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts
Jason P Kurs, Manuele Simi, Fabien Campagne doi:...
Forum: RNA Sequencing 01-07-2016, 09:36 AM
Replies: 0
Views: 836
Posted By Fabien Campagne
mini-survey: effort in teaching beginners RNA-Seq data analysis

I'd like to measure the effort typically involved in teaching beginners basic gene expression data analysis (e.g., RNA-Seq). I have some ideas of course from teaching at our institution, but I am...
Forum: RNA Sequencing 01-16-2015, 11:43 AM
Replies: 0
Views: 919
Posted By Fabien Campagne
MetaR: a simple language useful for RNA-Seq data analysis

Hello,

I wanted to introduce MetaR (http://metaR.campagnelab.org), a language to analyze RNA-Seq data and produce visualizations such as heatmaps. MetaR provides a language simpler to learn and...
Forum: General 01-16-2015, 11:30 AM
Replies: 0
Views: 921
Posted By Fabien Campagne
Simpler data analysis with MetaR

Hello,

I wanted to introduce MetaR (http://metaR.campagnelab.org), a language to analyze RNA-Seq data and produce visualizations such as heatmaps. MetaR provides a language simpler to learn and...
Forum: Bioinformatics 07-20-2012, 12:12 PM
Replies: 2
Views: 1,359
Posted By Fabien Campagne
Goby 2.1

This release includes the following changes:

Improve compression of hybrid-1 codec by about 8% on average at similar speed. You can enable this improvement with option -x...
Forum: Bioinformatics 06-30-2012, 08:08 AM
Replies: 2
Views: 1,359
Posted By Fabien Campagne
Goby 2.0.1

We have released 2.0.1. This minor release includes responses to several suggestions we received about 2.0. Thanks to everybody who provided feedback. Here's the detailed list of changes:

...
Forum: Bioinformatics 06-15-2012, 05:39 AM
Replies: 2
Views: 1,359
Posted By Fabien Campagne
Goby 2.0 released

We are pleased to announce that Goby 2.0 (http://goby.campagnelab.org) has been released. Version 2 is a major milestone for the Goby project which brings state of the art alignment compression, very...
Forum: Bioinformatics 03-16-2012, 06:25 AM
Replies: 9
Views: 5,774
Posted By Fabien Campagne
Heng, you are right that Goby is lossy if you...

Heng, you are right that Goby is lossy if you compare to BAM because we throw out sequence and quality scores in regions that match exactly the reference.

I think the approach is quite different...
Forum: Bioinformatics 03-16-2012, 05:56 AM
Replies: 9
Views: 5,774
Posted By Fabien Campagne
There has been some confusion regarding Goby, the...

There has been some confusion regarding Goby, the file sizes it produces and what kind of data it keeps. I realize the confusion is likely due to problems in the conversion tool we provided with...
Forum: Bioinformatics 03-07-2012, 07:09 PM
Replies: 9
Views: 5,774
Posted By Fabien Campagne
Most tools working with BAM are likely to be...

Most tools working with BAM are likely to be slow. You could give the SNP caller provided with Goby (http://goby.campagnelab.org) a try. It is must faster than samtools, and can perform local...
Forum: Bioinformatics 10-05-2011, 05:25 AM
Replies: 12
Views: 3,661
Posted By Fabien Campagne
When the alignment is written in Goby format...

When the alignment is written in Goby format (which you can produce with this version of BWA (http://campagnelab.org/software/goby/bwa/), or with GobyWeb (http://gobyweb.campagnelab.org)), you can...
Forum: Bioinformatics 08-25-2011, 05:07 AM
Replies: 17
Views: 13,146
Posted By Fabien Campagne
You can also call genotypes for all sequences...

You can also call genotypes for all sequences positions with Goby. You will need the 'genotypes' output format of the discover-sequence-variants tool to get all sites sequenced.

See the tutorial...
Forum: Academic/Non-Profit Jobs 08-12-2011, 01:15 PM
Replies: 0
Views: 1,327
Posted By Fabien Campagne
post-doc NGS epigenetic research in neuroscience

The Campagne laboratory is located at the Weill Medical College of Cornell University, in the space of the Institute for Computational Biomedicine (http://icb.med.cornell.edu/). Our laboratory is...
Forum: Bioinformatics 06-14-2011, 05:46 AM
Replies: 0
Views: 1,063
Posted By Fabien Campagne
Java framework+tools Goby 1.9.7 released (fast realign near indels & capture stats)

We have released Goby 1.9.7. This release has several new features, including the option to realign reads around indels on the fly when running one of the discover-sequence-variant...
Forum: Bioinformatics 06-06-2011, 05:01 AM
Replies: 4
Views: 2,096
Posted By Fabien Campagne
Adding optional attributes to Goby alignment entries

I am not sure about BAM alignments, but it is possible to add custom 'tags' to Goby (http://campagnelab.org/software/goby/tutorials/developing-with-goby/) alignment entries. You would simply do:

...
Forum: Bioinformatics 04-29-2011, 05:21 AM
Replies: 0
Views: 1,303
Posted By Fabien Campagne
Goby 1.9.5 released, BWA, GSNAP, IGV2 support, VCF format, genotype calling and more

We have released Goby 1.9.5. Goby is a framework and tool box for efficient next-gen analysis (RNA-Seq, sequence variations including genotypes, allelic expression or estimation of methylation...
Forum: Bioinformatics 02-17-2011, 05:34 PM
Replies: 82
Views: 29,124
Posted By Fabien Campagne
Regarding Heng's 4), yes 80-90% smaller than BAM...

Regarding Heng's 4), yes 80-90% smaller than BAM is when quality scores are stored only for these bases that differ between the read and the reference, not for any flanking read sequence. This is...
Forum: Bioinformatics 02-17-2011, 04:10 AM
Replies: 82
Views: 29,124
Posted By Fabien Campagne
Thanks laura for a reference that should help...

Thanks laura for a reference that should help ties this discussion together. We have used the reference in Goby only to compress alignments (Michael.James.Clark points are well received, this is not...
Forum: Bioinformatics 02-16-2011, 06:38 PM
Replies: 82
Views: 29,124
Posted By Fabien Campagne
fpepin is perfectly correct about the compression...

fpepin is perfectly correct about the compression approach. We have been using this approach in the Goby alignment format for about two years (see...
Forum: Bioinformatics 12-17-2010, 04:50 AM
Replies: 0
Views: 1,060
Posted By Fabien Campagne
Goby tools and APIs 1.9 released

Hello,
We have just released Goby 1.9. This version now provides APIs to access only a slice of an alignment, where the slice is defined by the alignment entries contained between two position on...
Forum: Bioinformatics 12-17-2010, 04:40 AM
Replies: 0
Views: 1,928
Posted By Fabien Campagne
Support for parallelization of paired-end alignments with BWA

Hello,

bwa aln is multi-threaded, but the sampe step needed to combine results for paired-end reads is not. We have released a version of BWA modified to natively support Goby...
Forum: Core Facilities 11-04-2010, 02:43 PM
Replies: 0
Views: 1,890
Posted By Fabien Campagne
GobyWeb web application for alignment and differential expression analysis

Hello,

We have developed this tool for internal use, but I wonder if it would be of interest to core facilities and their users as well:
http://gobyweb.campagnelab.org
...
Forum: Bioinformatics 11-04-2010, 02:25 PM
Replies: 0
Views: 1,395
Posted By Fabien Campagne
Java framework Goby 1.8 released

Goby (http://goby.campagnelab.org) is a Java framework and set of tools for storing and analyzing next-gen data. We have just released version 1.8 of the framework. Significant changes include:
...
Forum: Bioinformatics 06-17-2010, 08:38 AM
Replies: 3
Views: 6,933
Posted By Fabien Campagne
Goby supports Upper Quartile normalization since...

Goby supports Upper Quartile normalization since version 1.5. See argument --normalization-methods at...
Showing results 1 to 25 of 39

 


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