known miRNAs and bigwig options are not working #175
Description
Using the newest Shortstack build, alignments outputs etc all work, however the known miRNAs and bigwig options are not recognized, command:
ShortStack
--readfile "$INPUT_DIR/$FILE"
--genomefile "$GENOME"
--outdir "$OUT_DIR/$BASENAME"
--threads 10
--known_miRNAs /net/queitsch/vol1/home/cuperusj/Molly_smalLRNA/Hybrid_smallRNA_120225/Zm_mature_miRNAs.fa
--make_bigwigs
ShortStack version 4.1.2
Beginning run
Options:
{ 'adapter': None,
'align_only': False,
'autotrim': False,
'autotrim_key': 'TCGGACCAGGCTTCATTCCCC',
'autotrim_only': False,
'bamfile': None,
'dicermax': 24,
'dicermin': 21,
'dn_mirna': False,
'genomefile': '/net/queitsch/vol1/home/cuperusj/Molly_smalLRNA/Hybrid_smallRNA_120225/B73_and_Mo17.fa',
'known_miRNAs': None,
'locifile': None,
'locus': None,
'make_bigwigs': False,
'mincov': 1,
'mmap': 'u',
'nohp': False,
'outdir': '/net/queitsch/vol1/home/cuperusj/Molly_smalLRNA/Hybrid_smallRNA_120225/ShortStack_runs/B73_1',
'pad': 200,
'readfile': [ '/net/queitsch/vol1/home/mperch/Sequencing_data/QC_IlluminaSeq/120125_smRNA_B73_Mo17/B73_1.fastq'],
'strand_cutoff': 0.8,
'threads': 10}