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Forum: Bioinformatics 03-21-2017, 07:43 AM
Replies: 0
Views: 837
Posted By ameyer
Registration deadline for CBW advanced bioinformatics workshops fast approaching

The registration deadline for the bioinformatics.ca workshops (https://bioinformatics.ca/workshops-2017) for 2017 is **April 3rd**. Submit an application...
Forum: Bioinformatics 04-13-2016, 05:22 AM
Replies: 0
Views: 1,489
Posted By ameyer
Register today for advanced bioinformatics training workshops this summer

Informatics and Statistics for Metabolomics (http://bioinformatics.ca/workshops/2016/informatics-and-statistics-metabolomics-2016) Early Registration April 25, 2016 Workshop Start May 26, 2016
...
Forum: Events / Conferences 01-27-2016, 07:55 AM
Replies: 0
Views: 1,175
Posted By ameyer
Population and Quantitative Genomics Workshop in Toronto

Canadian Bioinformatics Workshops has developed a 2-day workshop that focuses on the genetics and analysis of genomes and quantitative traits in human populations, with emphasis on population genetic...
Forum: Events / Conferences 01-27-2016, 07:49 AM
Replies: 0
Views: 930
Posted By ameyer
Bioinformatics on Big Data: Computing on the Human Genome Workshop in Toronto

Canadian Bioinformatics Workshops has developed a 2-day course providing an introduction to security and privacy issues related to working on human genome data and the processes necessary to access...
Forum: Events / Conferences 01-27-2016, 07:41 AM
Replies: 0
Views: 911
Posted By ameyer
Analysis of Metagenomic Data Workshop in Vancouver

Canadian Bioinformatics Workshops has developed a 3-day course providing an introduction to metagenomic data analysis followed by hands-on practical tutorials demonstrating the use of metagenome...
Forum: Events / Conferences 01-27-2016, 07:34 AM
Replies: 0
Views: 982
Posted By ameyer
Epigenomic Data Analysis Workshop in Toronto

Canadian Bioinformatics Workshops has developed a 2-day course providing an introduction to ChIP-seq and WGBS data analysis followed by integrated tutorials demonstrating the use of popular ChIP-Seq...
Forum: Events / Conferences 01-27-2016, 07:28 AM
Replies: 0
Views: 941
Posted By ameyer
Informatics for RNA-Seq Analysis Workshop in Toronto

Canadian Bioinformatics Workshops has developed a 2-day course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis...
Forum: Events / Conferences 01-27-2016, 07:20 AM
Replies: 0
Views: 874
Posted By ameyer
Pathway and Network Analysis of -omics Data in Toronto

Canadian Bioinformatics Workshops has developed a 2.5-day course covering the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information. The...
Forum: Events / Conferences 01-27-2016, 07:12 AM
Replies: 0
Views: 886
Posted By ameyer
Informatics on High-Throughput Sequencing Data Workshop in Montreal

Canadian Bioinformatics Workshops has developed a popular 2-day course covering the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on...
Forum: Events / Conferences 01-27-2016, 07:01 AM
Replies: 0
Views: 941
Posted By ameyer
Introduction to R and Exploratory Analysis of Biological Data Using R Workshops

Canadian Bioinformatics Workshops is offering two workshops on using R: a one-day Introduction to R workshop (June 6, 2016) and a two-day Exploratory Analysis of Biological Data using R workshop...
Forum: Events / Conferences 01-27-2016, 06:52 AM
Replies: 0
Views: 1,146
Posted By ameyer
Bioinformatics for Cancer Genomics

Canadian Bioinformatics Workshops has developed a 5-day workshop covering the key bioinformatics concepts and tools required to analyze cancer genomic data sets. Participants will gain experience in...
Forum: Events / Conferences 01-27-2016, 06:47 AM
Replies: 1
Views: 1,248
Posted By ameyer
Informatics and Statistics for Metabolomics

Canadian Bioinformatics Workshops is offering a 2-day workshop on Informatics and Statistics for Metabolomics May 26 - May 27, 2016 in Toronto, Ontario. The workshop will cover many topics ranging...
Forum: Events / Conferences 01-11-2016, 10:34 AM
Replies: 0
Views: 1,113
Posted By ameyer
Announcing the Canadian Bioinformatics Workshop Series for 2016

Dear Colleagues,

Kick start the new year with a bioinformatics workshop! Bioinformatics.ca continues to offer data analysis driven workshops in the most current research areas.

New for 2016:...
Forum: Bioinformatics 10-01-2012, 09:59 AM
Replies: 0
Views: 1,135
Posted By ameyer
Ambiguous bases vs mismatches in Tophat

Does Tophat treat ambiguous bases (N) in the reference as mismatches? In the Tophat manual -N/--read-mismatches is defaulted to 2 but there doesn't seem to be a parameter to set the number of...
Forum: RNA Sequencing 06-27-2012, 05:08 AM
Replies: 25
Views: 6,019
Posted By ameyer
I didn't specify what my library type was so I...

I didn't specify what my library type was so I don't think this is causing the error. Have you tried emailing the creators of Cufflinks?
Forum: RNA Sequencing 06-25-2012, 08:30 AM
Replies: 25
Views: 6,019
Posted By ameyer
Error when using Cufflinks 2.0.1

Hi,
When running Cufflinks 2.0.1 it generates the error:

*** glibc detected *** cufflinks: double free or corruption (!prev): 0x000000003f909d00 ***
======= Backtrace: =========...
Forum: RNA Sequencing 05-13-2011, 08:54 AM
Replies: 1
Views: 1,778
Posted By ameyer
SamTools and allelic expression

Hi,
I have RNA-seq reads from Illumina and I have used TopHat to align them. I have reads from two inbred parents and two hybrid offspring. I have used SamTools mpileup to find SNPs between the...
Forum: RNA Sequencing 03-16-2011, 04:53 AM
Replies: 5
Views: 2,804
Posted By ameyer
Thanks for the link however the file only seems...

Thanks for the link however the file only seems to contain entries for chromosome 9...
Forum: RNA Sequencing 03-15-2011, 08:19 AM
Replies: 5
Views: 2,804
Posted By ameyer
GTF file for maize?

Hi,
Is there a GTF file for maize? I know a GFF file exists but I'm using Cufflinks and need the GTF.
Thanks,
Ann
Forum: Bioinformatics 03-01-2011, 07:51 AM
Replies: 10
Views: 4,474
Posted By ameyer
The only colons that are allowed in the @SQ lines...

The only colons that are allowed in the @SQ lines are the ones directly after SN and LN so the one you have between EG and bd would have to be removed. It would also have to be removed in all the...
Forum: Bioinformatics 03-01-2011, 06:39 AM
Replies: 10
Views: 4,474
Posted By ameyer
Tech support was able to find the cause of my...

Tech support was able to find the cause of my error in my SAM file. In the header section I had some colons as part of my contig names that messed up Cufflinks. By removing the colons in the header...
Forum: Bioinformatics 02-28-2011, 04:42 AM
Replies: 10
Views: 4,474
Posted By ameyer
Me too

I've had this error as well. I emailed the help email address and they said it's a rare issue with the software where the contig names have hash collisions. The problem should be fixed when they...
Forum: Bioinformatics 02-24-2011, 07:20 AM
Replies: 1
Views: 1,172
Posted By ameyer
Cufflinks error

Hi,
I'm having a problem getting Cufflinks to run.
I used TopHat to align my reads but when running Cufflinks it gives the error:
Error: sort order of reads in BAMs must be the same.
I've tried...
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