Gene deserts

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...

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Mapping random sized reads to the genome

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...

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