mappability 150bp reads

[wdecoster]

Dear,

Could you give me instructions on how to generate a mappability bed file for 2x 150bp NextSeq reads?

Regards,
Wouter

[rgcgithub]

You would have to create one from scratch (as there doesn't appear to be a precomputed one on UCSC) using the program GEM (http://algorithms.cnag.cat/wiki/The_GEM_library) or something similar.

Alternatively, you may consider just using the precomputed 100mer mappability track, as the number of exons that fail 100mer vs 150mer mappability <75% is likely quite low. Note that mappability is only used to filter exons from consideration, so matching it exactly to your sequencing protocol is not essential. Matching the INSERT_SIZE parameter used in the annotate_windows.sh script is more important.

Evan