A Nextflow pipeline to use samtools and WASP to get ASE summary data.
-
Set the variables within the ase_pipeline.nf file in the Configuration for the specific run section, and anything needed for the pipeline.
-
External programs are not included, but can be downloaded publicly and added to a "/bin" folder. They should be: -WASP -your aligner -Samtools
-
Edit the ase_pipeline.nf process 'remap' to match your aligner and the arguments for the aligner.