Index

Symbols

-c, --cutadapt <cutadapt> CLI-Reference-compile-step-stats command line option -d, --dedup <dedup> CLI-Reference-compile-step-stats command line option -f, --filter <filter> CLI-Reference-compile-step-stats command line option -i, --inbed <inbed> CLI-Reference-dedup command line option -i, --inputstats <inputstats> CLI-Reference-stats-percentage command line option -l, --log <log> CLI-Reference-bt2-log-to-csv command line option -n, --name <name> CLI-Reference-bt2-log-to-csv command line option CLI-Reference-compile-step-stats command line option CLI-Reference-sum-stats command line option

-o, --out <out> CLI-Reference-bt2-log-to-csv command line option CLI-Reference-compile-step-stats command line option CLI-Reference-merge-bowtie2-logs command line option CLI-Reference-merge-concat-csv command line option CLI-Reference-merge-overall-stats command line option CLI-Reference-stats-percentage command line option CLI-Reference-sum-stats command line option -o, --outbed <outbed> CLI-Reference-dedup command line option -p, --prefix <prefix> CLI-Reference-bt2-log-to-csv command line option -q, --quality <quality> CLI-Reference-compile-step-stats command line option -t, --trans <trans> CLI-Reference-compile-step-stats command line option

C

CLI-Reference-bt2-log-to-csv command line option -l, --log <log> -n, --name <name> -o, --out <out> -p, --prefix <prefix> CLI-Reference-compile-step-stats command line option -c, --cutadapt <cutadapt> -d, --dedup <dedup> -f, --filter <filter> -n, --name <name> -o, --out <out> -q, --quality <quality> -t, --trans <trans> CLI-Reference-dedup command line option -i, --inbed <inbed> -o, --outbed <outbed>

CLI-Reference-merge-bowtie2-logs command line option -o, --out <out> INPUT_LOG_PATHS CLI-Reference-merge-concat-csv command line option -o, --out <out> INPUT_CSVS CLI-Reference-merge-overall-stats command line option -o, --out <out> INPUT_STATS CLI-Reference-stats-percentage command line option -i, --inputstats <inputstats> -o, --out <out> CLI-Reference-sum-stats command line option -n, --name <name> -o, --out <out> INPUT_STATS

I

INPUT_CSVS CLI-Reference-merge-concat-csv command line option INPUT_LOG_PATHS CLI-Reference-merge-bowtie2-logs command line option

INPUT_STATS CLI-Reference-merge-overall-stats command line option CLI-Reference-sum-stats command line option