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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Mapping qualities

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…

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Using blat to map short RNAs

Updated on 2013 November 5th to include mapping of piRNAs I still use blat as my multi-purpose alignment tool despite it being developed over 10 years ago. For those needing a simple introduction to blat, see my using blat post. Now I was wondering if blat could aligned short RNAs; the definition of short RNAs…

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