Repeatmasker files:
http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=609943691_XL6bH3XztTXX6uXDmha6A7j1WuU8&boolshad.hgta_printCustomTrackHeaders=0&hgta_ctName=tb_rmsk&hgta_ctDesc=table+browser+query+on+rmsk&hgta_ctVis=pack&hgta_ctUrl=&fbQual=whole&fbUpBases=200&fbDownBases=200&hgta_doMainPage=cancel

ouput format: bed for mm9_rmsk.bed.gz
selected fields from table for: mm9_rmsk_info


Gencode gtf file for mm9:
https://www.gencodegenes.org/releases/11.html


add to PATH
PATH=/data/images/proton/DKlab/mr/parclip/parpipe/bpipe/bpipe-master/bin:$PATH; export PATH
PATH=/data/results/tools/align/bowtie-0.12.9:$PATH; export PATH
PATH=/home/reczko/a/tools/clip/bpipe-0.9.9.2/bin:$PATH; export PATH
PATH=/data/results/tools/adapter/cutadapt-1.9.1/bin:$PATH; export PATH
reczko@max:/data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master$ ./setup.sh -s h
reczko@max:/data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/test$ bpipe run -r ../parclip_pipe.sh test.fastq



reczko@max:/data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/test$ head -999 test.sam  | tail -3
1729-97	0	GL000220.1	158544	255	22M	*	0	0	TTCTCTCGGGGCCACGCGCGCG	IIIIIIIIIIIIIIIIIIIIII	XA:i:0	MD:Z:22	NM:i:0
reczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_5$ head test.sam 
545_4189_4380_F3	0	chr17	71313013	0	49M	*	0	0	ACAGGTTAGTTTTACCCTACTGATGATGTGTTGTTGCCATGGTAATCCT	qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq	NM:i:0	X0:i:3	MD:Z:49