Making slides using R

Updated 2015 January 14th I'll be giving a talk on analysing CAGE data using R in an upcoming workshop held at our institute early next year. I thought it would be a good time to check out slidify, which is an R package that can create HTML slides from R Markdown, since I'm planning on...

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CAGE analysis using the R Bioconductor package CAGEr

This post is outdated; please refer to the official documentation. Cap Analysis Gene Expression (CAGE) is a molecular technique, developed at RIKEN, which captures all transcription starting sites (TSSs) of an RNA population. The C in CAGE refers to the altered nucleotide at the 5' site of precursor messenger RNA, termed the cap, which CAGE...

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Encyclopedia of DNA elements (ENCODE)

ENCODE is an abbreviation of "Encyclopedia of DNA elements", a project that aims to discover and define the functional elements encoded in the human genome via multiple technologies. Used in this context, the term "functional elements" is used to denote a discrete region of the genome that encodes a defined product (e.g., protein) or a...

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Clustering mapped reads

Updated 2014 October 8th to include an analysis using CAGE data from ENCODE and rewrote parts of the post. In this post I will write about a read clustering method called paraclu, which allows mapped reads to be clustered together. This is particularly useful when working with CAGE data, where transcription start sites (TSSs) are...

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Visualising FANTOM3 human CAGE data

First download the relevant tables from here. Download tss_library_expr_summary.tsv.bz2, tss_summary.tsv.bz2 and rna_lib_summary.tsv.bz2 and bunzip2 the files. According to information derived from rna_lib_summary.tsv there are 13,897 CAGE tags from the prostate gland (rna_lib_id = HBA). Double check this: Genomic coordinates of TSSs can be obtained from tss_summary.tsv. Here's a script which generates bedgraph files of all...

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