Question about multimapping reads

[amitjavilaventura]

Hi,

I would like to try PILFER to predict piRNA clusters in three distinct species, but I have some questions about multi-mapping reads.

• Does PILFER work with multi-mapping reads? If so, how many alignments per read is the maximum allowed?
• It is possible to "reallocate" multimapping reads? With "reallocate" I mean weight each alignment of a multi-mapping read based on the density of reads in the surrounding region.
• In case the answer to the previous questions is "yes", does PILFER works only with Bowtie or it can work with other not standalone mappers, such as sRNAmapper.pl (the mapper used in the prediction with proTRAC).

Thank you very much.

Best regards,
Adrià.