At this moment here are three files:
1) valid_gtf.pl
2) mRNA2genomeBAM.pl
3) example.sh
4) take_fasta_from_gtf.pl
5) wig_parse.pl
6) correct_gtf_chains.pl

valid_gtf.pl
    validation of gtf is neeeded when our transcript names differin BAM and gtf.
At now 'valid_gtf.pl' takes standard GoldenPath RefGene.txt and creates file
for Bowtie.
    You have to keep in mind that fact that output of 'main_current.pl' now is
in SAM format, so after it's job have be done, you need to create BAM, sort it
and then make index file. for samtools, it will be as:

$ samtools view -bS output.sam > output.bam
$ samtools sort output.bam output_sorted
$ samtools index output_sorted.bam


mRNA2genomeBAM.pl
    Usage of mRNA2genomeBAM.pl is described in it's help. Try '-h' or '--help'.

TAKE_FASTA_FROM_GTF.PL
    This script makes fasta RefSeq file from validated GTF files and genome reference

WIG_PARSE.PL
    This script parses WIG file and create GTF table that contains raws with continious
regions. Actually, it's a very simple peakfinder

correct_gtf_chains.pl
    Made for poor peakfinders that don't track directions of reads in peaks.

some other scripts
NOTES

DEPENDENCIES

samtools
libbio-perl-samtools
perl :)


TODO

1. make correct_gtf_chains.pl to work
2. Some tetriary analisys scripts for validate new undescribed transcripts and miRNAs
3. statistical analisys for differential expression levels for peaks and transcripts