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broadinstitute / catch

A package for designing compact and comprehensive capture probe sets.
MIT License
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Add option to filter probes with poly(A) sequence #22

Closed haydenm closed 5 years ago

haydenm commented 5 years ago

This adds the polya_filter module, which is a filter on probes that contain sequence with long stretches of A bases (or T bases). It might be desirable to avoid such probe sequences, e.g., to not enrich carrier RNA.

This also adds a --filter-polya argument to design.py that, when set, applies the polya_filter module.

The definition of a stretch of A bases (or T bases) given as arguments with --filter-polya.

coveralls commented 5 years ago

Coverage Status

Coverage increased (+0.06%) to 95.07% when pulling 712e47f0eb32e0605d3e31cd52dec1773f96e310 on filter-polya into 90d7b9b45546d667c0f7c28677738df2b4b4b575 on master.