LINE1-insertion-mapping

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.

1. bowtie2 for read2 single end alingment
2. bowtie2 for paired end alignment
3. novoalign for read2 single end alignment
4. 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;