
#####  b8 library, YES CATG required 
python /mnt/wigclust5/data/safe/kendall/stillman02/nla3.fastq.gel.pairs01.py /mnt/wigstore5/user/kendall/stillman02/b8/alu.fastq.steam01.log.txt /mnt/wigstore5/user/kendall/stillman02/b8/alu.fastq.steam01.stat.b8.txt <(gunzip -c /mnt/wigclust20/data/safe/sili/yeast01/b8/r1.fastq.gz) <(gunzip -c /mnt/wigclust20/data/safe/sili/yeast01/b8/r2.fastq.gz) /mnt/wigstore5/user/kendall/stillman02/b8/r1.fastq  /mnt/wigstore5/user/kendall/stillman02/b8/r2.fastq > /mnt/wigstore5/user/kendall/stillman02/b8/alu.fastq.stream01.stdout /mnt/wigclust5/data/safe/kendall/stillman02/nla3.barcodes02.txt

#####  gzip commands
gzip -1 /mnt/wigstore5/user/kendall/stillman02/b8/r1.fastq
gzip -1 /mnt/wigstore5/user/kendall/stillman02/b8/r2.fastq

####  new b8 
/mnt/wigclust24/data/safe/kendall/hisat2-2.1.0/hisat2 -p 14 -3 0 -5 0 -X 2000 --no-spliced-alignment --met-file /mnt/wigstore5/user/kendall/stillman02/b8/hisat2pe_metrics.txt -x /mnt/wigclust24/data/safe/kendall/hisat2-2.1.0/indexes/sc3 -1 <(gunzip -c /mnt/wigstore5/user/kendall/stillman02/b8/r1.fastq.gz) -2 <(gunzip -c /mnt/wigstore5/user/kendall/stillman02/b8/r2.fastq.gz) | samtools view -Sbh - | samtools sort -o /mnt/wigstore5/user/kendall/stillman02/b8/hisat2pe_sorted.bam - 

samtools view /mnt/wigstore5/user/kendall/stillman02/b8/hisat2pe_sorted.bam | python /mnt/wigclust5/data/safe/kendall/pythonpgms/alu.split.sam.hisat2.pe01.py | sort -S 32G -k 1,1 -k 2,2 -k 3,3n -k 4,4n -k 6,6 -k 5,5 > /mnt/wigstore5/user/kendall/stillman02/b8/hisat2pe_sorted.maplocs_2.txt

cat /mnt/wigstore5/user/kendall/stillman02/b8/hisat2pe_sorted.maplocs_2.txt | python /mnt/wigclust5/data/safe/kendall/pythonpgms/alu.stream.beadtags.geN.pe01.py 200 > /mnt/wigstore5/user/kendall/stillman02/b8/b8_temp.maplocs.sorted.dedup.hisat.txt

cat /mnt/wigstore5/user/kendall/stillman02/b8/b8_temp.maplocs.sorted.dedup.hisat.txt | cut -f 2,3 | sort -S 6G -k 1,1 -k 2,2n > /mnt/wigstore5/user/kendall/stillman02/b8/b8.maplocs.sorted.dedup.hisat.txt


#####   varbin hisat  b8 
#cat /mnt/wigstore5/user/kendall/stillman02/b8/b8_temp.maplocs.sorted.dedup.hisat.txt | python /mnt/wigclust5/data/safe/kendall/pythonpgms/gel_20180928.varbin.hg19.Nk.v4.py /mnt/wigclust5/data/safe/kendall/stillman02/hg19.bin.boundaries.1_25k.hisat.gel_20180930.sorted.txt /mnt/wigstore5/user/kendall/stillman02/b8 .hg19.1_25k.k50.varbin.hisat.txt /mnt/wigstore5/user/kendall/stillman02/b8/b8.varbin.hisat.1_25k.stats.txt /mnt/wigstore5/user/kendall/stillman02/b8/b8.varbin.hisat.1_25k.log.txt 100000

#cat /mnt/wigstore5/user/kendall/stillman02/b8/b8_temp.maplocs.sorted.dedup.hisat.txt | python /mnt/wigclust5/data/safe/kendall/pythonpgms/gel_20180928.varbin.hg19.Nk.v4.py /mnt/wigclust5/data/safe/kendall/stillman02/hg19.bin.boundaries.5k.hisat.gel_20180930.sorted.txt /mnt/wigstore5/user/kendall/stillman02/b8 .hg19.5k.k50.varbin.hisat.txt /mnt/wigstore5/user/kendall/stillman02/b8/b8.varbin.hisat.5k.stats.txt /mnt/wigstore5/user/kendall/stillman02/b8/b8.varbin.hisat.5k.log.txt 150000

#cat /mnt/wigstore5/user/kendall/stillman02/b8/b8_temp.maplocs.sorted.dedup.hisat.txt | python /mnt/wigclust5/data/safe/kendall/pythonpgms/gel_20180928.varbin.hg19.Nk.v4.py /mnt/wigclust5/data/safe/kendall/stillman02/hg19.bin.boundaries.20k.hisat.gel_20180930.sorted.txt /mnt/wigstore5/user/kendall/stillman02/b8 .hg19.20k.k50.varbin.hisat.txt /mnt/wigstore5/user/kendall/stillman02/b8/b8.varbin.hisat.20k.stats.txt /mnt/wigstore5/user/kendall/stillman02/b8/b8.varbin.hisat.20k.log.txt 600000
