cutadapt parameters:
-a TCGTATGCCGTCTTCTGCTTG -g AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC -b CGTACGCGGGTTTAAACGA -b CGTACGCGGAATAGTTTAAACTGT -n 1 -m 20

bowtie parameters:
-v 1 -m 10 --all --best --strata

PARalyzer parameters (.ini file settings):
BANDWIDTH=3
CONVERSION=T>C
MINIMUM_READ_COUNT_PER_GROUP=2
MINIMUM_READ_COUNT_PER_CLUSTER=2
MINIMUM_READ_COUNT_FOR_KDE=3
MINIMUM_CLUSTER_SIZE=11
MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=2
MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=2
MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=1
MINIMUM_READ_LENGTH=20
MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=0


Annotation priority (.yaml file):
# Comments are allowed and are indicated with the pound (aka octothorpe) symbol
# Higher numeric value indicates higher priority
trailing annotation:
coding:
  aligned:
    show     : false
    priority : 13

3'utr:
  aligned:
    show     : false
    priority : 12

  downstream:
    show     : false
    region   : 1000

5'utr:
  aligned:
    show     : false
    priority : 11

  upstream:
    show     : false
    region   : 1000

tss:
  aligned:
    show     : false
    priority : 1


tes:
  aligned:
    show     : false
    priority : 1

 
intron:
  aligned:
    show     : false
    priority : 7

lincRNA:
  aligned:
    show     : false
    priority : 6

piRNA:
  aligned:
    show     : false
    priority : 5

miRNA:
  aligned:
    show     : false
    priority : 8

rRNA:
  aligned:
    show     : false
    priority : 40

snoRNA:
  aligned:
    show     : false
    priority : 34

snRNA:
  aligned:
    show     : false
    priority : 33

miscRNA:
  aligned:
    show     : false
    priority : 19

Mt rRNA:
  aligned:
    show     : false
    priority : 22


Mt tRNA:
  aligned:
    show     : false
    priority : 21


tRNA:
  aligned:
    show     : false
    priority : 30


repeat:
  aligned:
    show     : false
    priority : 29