Usage: <read1.fq> <read2.fq> <TF_to_scan>; : options can be combined without spaces in between (i.e. 12, 123 or 1234); Mapping database is hg19.
- bowtie2 for read2 single end alingment
- bowtie2 for paired end alignment
- novoalign for read2 single end alignment
- novoalign for paired end alignment <TF_to_scan>: underscore delimited transcription factors to scan;
Output name: prefix is from the first "-"(hyphen) deliminated input name;