BEDTools puzzles

Updated 2015 December 16th: the files for the puzzles can be downloaded from the Amazon cloud Roughly two weeks ago I came across this excellent BEDTools tutorial and saw some puzzles or homework questions at the end of the tutorial; naturally I tweeted about it: Oh this looks like fun; BEDTools puzzles http://t.co/UMowwdPLEf— Dave Tang...

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Defining genomic regions

Updated 2014 June 24th to use GENCODE version 19 RNA sequencing (RNA-Seq) reads are typically mapped back to the genome (or transcriptome in some cases) after sequencing. The next task is to annotate the reads, to see which regions the reads mapped to. Typically one creates an annotation file and compares the coordinates of the...

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