Computational biology and genomics
Find regions of the mouse genome devoid of any annotation (ESTs, mRNA, repeats, RefSeq and UCSC genes). Annotation tracks downloaded using the table browser feature of the UCSC Genome Browser. Chromosome sizes of mm9 downloaded from here. Code for finding regions of 10kb devoid of any annotation. In the mm9 genome I found 9,634 10kb…
Simple question, what are the mapping statistics for random pieces of DNA of size 10 to 30 to the human genome? Generate 1,000,000 random pieces of DNA from size 10 to 30: Map to the hg19 genome using BWA with up to 2 mismatches: Generate statistics from the BAM file Some statistics: Number of unmapped…
2014 June 6th: Major rewrite of post The Burrows-Wheeler Aligner (BWA) is a popular short read alignment program. Here I test the program with an artificial reference sequence. First download and compile the program: