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Monthly Archives: September 2011
Using bins when comparing genomic features
Comparing two files containing genomic features is a common task e.g. finding out whether the coordinates of your tags intersect with genes. Of course you could use intersectBed (as part of the BEDTools suite) for this purpose but here’s how … Continue reading
Analysis of the complement and molecular evolution of tRNA genes in cow
Step by step analysis of defining the tRNA repertoire in the bovine genome (in the most recent version) based on the procedure published in this article. 1. Download bosTau5.fa.gz from http://hgdownload-test.cse.ucsc.edu/goldenPath/bosTau5/bigZips/ and gunzip 2. Download and install tRNAscan-SE from http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz … Continue reading
Bidirectional genes
Download 5′ UTR for all RefSeq genes using the UCSC Table Browser. Separate features according to strand Use intersectBed to find overlapping features Performing a GO enrichment analysis on the unique list of bidirectional genes and using all the genes … Continue reading
Mapping qualities
Short read alignment programs, such as bwa, usually have a mapping quality score for each read that is aligned to a reference. I came across this useful post in seqanswers and here I try to replicate it with an example … Continue reading
Using Velvet
Write script for generating random tags from a longer piece of DNA Generate random tags and use as input for velvet I don’t know why in the definition line reads length = 480 (NODE_1_length_480) when the contig length is 500. … Continue reading