NETseq alignment scripts for Methods in Molecular Biology v1.0

Initial code release.
 
This code is part of a manuscript accepted for publication in Methods in Molecular Biology:
Profiling metazoan transcription genome-wide with nucleotide resolution using native elongating transcript sequencing
Danya J. Martell, Robert Ietswaart, Brendan M. Smalec, and L. Stirling Churchman
Here we provide the custom alignment pipeline that is used to generate (human) NET-seq coverage files as described in Martell et al, Methods in Molecular Biology (accepted). Considerable improvements have been made which increase the final coverage 2-3x as compared to the previous NETseq alignment pipelines. Here, we also include code for when a Drosophila live cell spike in was used (see publication for experimental details).
When you use this code repository in a publication, please cite the zenodo DOI for this software until the above mentioned manuscript has been formally published. Once the manuscript is published, please then cite the MiMB publication instead.