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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.
The text was updated successfully, but these errors were encountered:
Hi,
I would like to try PILFER to predict piRNA clusters in three distinct species, but I have some questions about multi-mapping reads.
PILFER
work with multi-mapping reads? If so, how many alignments per read is the maximum allowed?PILFER
works only withBowtie
or it can work with other not standalone mappers, such assRNAmapper.pl
(the mapper used in the prediction withproTRAC
).Thank you very much.
Best regards,
Adrià.
The text was updated successfully, but these errors were encountered: