Computational biology and genomics
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 to do it anyway using Perl. NOTE: I hard code the length of my tags…
Step by step analysis of identifying the bovine tRNA repertoire (using the most recent version of the bovine genome) based on the procedure published in this article. This was my first first-authored paper (published as part of the bovine genome companion papers), and in retrospect there could have been many improvements, however the paper was…
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 as the universe list: Although this was a brief analysis, the results are somewhat similar…
Updated 2014 December 17th Current high throughput sequencers produces reads that are short; for example the HiSeq2000 produces millions of reads that are 50 and 100 bp long. To align such short reads with high speed and accuracy, many short read alignment programs have been developed, such as BWA. The major limitation is the length…
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. BLAST the contig back to the original sequence Score = 924 bits (500), Expect =…