Examples for mm10 are in: /isilon_temp/garber/genome_data/mouse/mm10/

1) genome.fa:	get genome (from UCSC?) as genome.fa
2) genome.fa.fai:	create fai index using samtools and genome.fa
3) *bt2:		create (or donwload if available) bowtie2 indexes from genome.fa using bowtie2
4) *ebwt:		if ribosomal sequence is available somehow - create bowtie1 indexes from it. Otherwise skip mapping to ribosome
5) ucsc.gtf:	download from UCSC "ucsc genes" (knownGene) from table browser in gtf format. If ucsc genes are not available - use other track (refseq?) and just rearrange columns as in example from mm10.
6) knownIsoforms.txt:	get it from UCSC (under ucsc genes).  should not be used... if something fails besause of it - please let me know :)
7) ref_flat:		download from UCSC ucsc genes (knownGene) from table browser in "all fields" format and rearrange columns as in example from mm10. If ucsc genes are not available - use other track (refseq?) and just rearrange columns as in example from mm10.
8) ucsc_into_genesymbol:	ucsc gene names are not very fancy. if conversion into official gene symbol is desired- download ucscgenes->kgXref table and create one as in example. alternatively, if transcript names are fine - just create a file with two identical columns.
9) cuffcmp.combined.gtf:	/isilon_temp/garber/bin/cufflinks-2.1.1.Linux_x86_64/cuffcompare -s /path/to/genome.fa -CG -r ucsc.gtf ucsc.gtf.

if 4) is impossible to perform due to absence of ribosomal sequences, MASTERnoribosome.pl should be run instead of MASTERshort.pl (i.e. files will be processed without ribosomoe mapping)


refACT.tab is just tab delimited BED file that contains chr/start/end/strand from "refFlat" and >=500bp