In order to enable an iCal export link, your account needs to have an API key created. This key enables other applications to access data from within Indico even when you are neither using nor logged into the Indico system yourself with the link provided. Once created, you can manage your key at any time by going to 'My Profile' and looking under the tab entitled 'HTTP API'. Further information about HTTP API keys can be found in the Indico documentation.
Additionally to having an API key associated with your account, exporting private event information requires the usage of a persistent signature. This enables API URLs which do not expire after a few minutes so while the setting is active, anyone in possession of the link provided can access the information. Due to this, it is extremely important that you keep these links private and for your use only. If you think someone else may have acquired access to a link using this key in the future, you must immediately create a new key pair on the 'My Profile' page under the 'HTTP API' and update the iCalendar links afterwards.
Permanent link for public information only:
Permanent link for all public and protected information:
This course covers several aspects of next generation sequencing (NGS) data analysis and visualization, ranging from general tasks such as quality control, alignment and genomic region matching to the more specific tasks such as peak detection (ChIP-seq) and finding differentially expressed genes (RNA-seq). The course consists of lectures and hands-on exercises. As the user-friendly Chipster software is used for the exercises, no prior knowledge of NGS data analysis or unix is required. This course is primarily targeted for researchers who already have NGS data, or who are planning to start such experiments soon.
Chipster integrates a comprehensive collection of analysis tools for high-throughput data such as microarrays, proteomics and NGS. For NGS data there is currently functionality for ChIP-seq, RNA-seq, miRNA-seq, methyl-seq and CNA-seq data (for details, please see NGS tool content). Users can save their analysis pipelines as reusable automatic workflows, and both workflows and analysis sessions can be shared with colleagues. Access to CSC's Chipster server is free of charge for Finnish universities.
Thursday April 26, 2012
Introduction to Chipster
Quality control and filtering reads (FastQC, FastX, PRINSEQ)
Alignment to reference genome (Bowtie, BWA, TopHat)
Manipulation of BAM files (Samtools)
Visualization of aligned reads in their genomic context (Chipster genome browser)
Matching genomic regions (BEDtools, HTSeq)
Friday April 27, 2012
ChIP-seq: Peak detection (MACS), retrieving nearby genes and performing pathway analysis for them.