Fix --preset parameters.

.TH chromap 1 "15 Sept 2021" "chromap-0.1.1 (r234)" "Bioinformatics tools"

.TH chromap 1 "17 Sept 2021" "chromap-0.1.1 (r234)" "Bioinformatics tools"

.SH NAME

.PP

chromap - fast alignment and preprocessing of chromatin profiles

.TP 10

.B chip 

Mapping ChIP-seq reads

.RB ( -l2000

.B --remove-pcr-duplicates --low_memory

.RB ( -l

.I 2000

.B --remove-pcr-duplicates --low-mem

.BR --BED ).

.TP

.B atac

Mapping ATAC-seq/scATAC-seq reads

.RB ( -l2000

.B --remove-pcr-duplicates --low_memory --trim-adapters

.RB ( -l 

.I 2000

.B --remove-pcr-duplicates --low-mem --trim-adapters --Tn5-shift

.B --remove-pcr-duplicates-at-cell-level

.BR --BED ).

.TP

.B hic

Mapping Hi-C reads

.RB ( -e4

.B -q1 --low_memory --split-alignment

.RB ( -e 

.I 4

.B -q

.I 1 

.B --low-mem --split-alignment

.BR --pairs ).