Program options for hisat2_splice_sites: usage: hisat2_extract_splice_sites.py [-h] [-v] [gtf_file] Extract splice junctions from a GTF file positional arguments: gtf_file input GTF file (use "-" for stdin) optional arguments: -h, --help show this help message and exit -v, --verbose also print some statistics to stderr ---------------------------------------------- Program options for hisat2_build: HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo) Usage: hisat2-build [options]* reference_in comma-separated list of files with ref sequences hisat2_index_base write ht2 data to files with this dir/basename Options: -c reference sequences given on cmd line (as ) --large-index force generated index to be 'large', even if ref has fewer than 4 billion nucleotides -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting -p number of threads --bmax max bucket sz for blockwise suffix-array builder --bmaxdivn max bucket sz as divisor of ref len (default: 4) --dcv diff-cover period for blockwise (default: 1024) --nodc disable diff-cover (algorithm becomes quadratic) -r/--noref don't build .3/.4.ht2 (packed reference) portion -3/--justref just build .3/.4.ht2 (packed reference) portion -o/--offrate SA is sampled every 2^offRate BWT chars (default: 5) -t/--ftabchars # of chars consumed in initial lookup (default: 10) --localoffrate SA (local) is sampled every 2^offRate BWT chars (default: 3) --localftabchars # of chars consumed in initial lookup in a local index (default: 6) --snp SNP file name --haplotype haplotype file name --ss Splice site file name --exon Exon file name --seed seed for random number generator -q/--quiet verbose output (for debugging) -h/--help print detailed description of tool and its options --usage print this usage message --version print version information and quit ---------------------------------------------- Program options for hisat2_exons: usage: hisat2_extract_exons.py [-h] [-v] [gtf_file] Extract exons from a GTF file positional arguments: gtf_file input GTF file (use "-" for stdin) optional arguments: -h, --help show this help message and exit -v, --verbose also print some statistics to stderr ----------------------------------------------