python make-trackhub.py examples/trackhub-template.txt trackFolder
usage: make-trackhub.py [-h] [-norm] [-bs BINSIZE] experiment_template trackname
trackFolder can be an existing or new folder in 00_UCSC_tracks
If trackFolder doesn’t exist, it will make one with all the appropriate stuff for a UCSC trackhub
If trackFolder does exist, it will append the lines for the new data to the trackDB.txt
This works for bed, bedpe, and bam.
python align.py examples/rna-seq-template.txt START -rsem -rmdup -trim_adaptors
usage: align.py [-h] [-t NTHREADS] [-trim_adaptors] [-rmdup] [-quality QUALITY] [-rsem] [-cufflinks] experiment_template {STAR,bwa,bowtie2}
python call_accessible_regions.py examples/peaks-template.txt
usage: call_accessible_regions.py [-h] [-t NTHREADS] [-p PVAL] [-mapq MAPQ] experiment_template