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Determining mappability of paired-end MNase-seq data

Hi all,

In the past, for single-end reads of a given length n, we would determine mappability by chopping up the genome to length n and map data back to genome using Bowtie2. Any insights into how to best deal with assessing the mappability of paired-end MNase seq data where fragment lengths are heterogeneous?

Any insights are welcome,

MSB

sequencing sequence alignment
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updated by Ram Ram • written by buckleyms • buckleyms

1 answer

If I recall this right the paper below has more insights into how to interpret this for paired end data:

Fast Computation and Applications of Genome Mappability Plos One (2012)

at the same time here is an neat write-up titled

The slow death of the term "uniquely mappable" in deep sequencing studies and resisting the "conservative" urge to toss out data

something to consider...

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updated by Ram Ram • written by Istvan Albert Istvan Albert

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