Author: Michael Love and Euphy Wu Last modified: Feb 26 2022 Version: 0.0.6

• r/4.1.0
• hisat2/2.2.1
• samtools/1.13
• wasp/2019-12
• bowtie/1.3.1
• mmseq/1.0.10a
• anaconda/2019.10

The following directory structure is needed:

anno
data
ht2_align
mmseq
quants
reads
wasp_cht
wasp_mapping
wasp2_counts
wasp2_tests

simpleRepeat_dm6_Aug2014.bed is from UCSC Genome Browser:

https://genome.ucsc.edu/cgi-bin/hgTables?db=dm6&hgta_group=varRep&hgta_track=simpleRepeat&hgta_table=simpleRepeat&hgta_doSchema=describe+table+schema

The Drosophila GTF file is downloaded from:

http:https://ftp.ensembl.org/pub/release-100/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.28.100.chr.gtf.gz