#errors (encoded by ".") are counted only in the first 20 colors
#/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o 0hrep1filt2 -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual 
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o 0hrep2filt2 -f 0hrep2/ugc_604_4_F3.csfasta -g 0hrep2/ugc_604_4_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o 0hrep3filt2 -f 0hrep3/ugc_604_7_F3.csfasta -g 0hrep3/ugc_604_7_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o  2hrep1filt2 -f  2hrep1/ugc_604_2_F3.csfasta -g  2hrep1/ugc_604_2_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o 2hrep2filt2 -f 2hrep2/ugc_604_5_F3.csfasta -g 2hrep2/ugc_604_5_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o 2hrep3filt2 -f 2hrep3/ugc_604_8_F3.csfasta -g 2hrep3/ugc_604_8_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o  6hrep1filt2 -f  6hrep1/ugc_604_3_F3.csfasta -g  6hrep1/ugc_604_3_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o 6hrep2filt2 -f 6hrep2/ugc_604_6_F3.csfasta -g 6hrep2/ugc_604_6_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o 6hrep3filt2 -f 6hrep3/ugc_604_9_F3.csfasta -g 6hrep3/ugc_604_9_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o  IL4filt2 -f  IL4/ugc_604_11_F3.csfasta -g  IL4/ugc_604_11_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o IFNfilt2 -f IFN/ugc_604_10_F3.csfasta -g IFN/ugc_604_10_F3.QV.qual
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o IGGfilt2 -f IGG/ugc_604_12_F3.csfasta -g IGG/ugc_604_12_F3.QV.qual


./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 0hrep1F-4p  0hrep1filt2_T_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c

#./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o IGG-4p IGG/ugc_604_12_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 0hrep1-4p  0hrep1/ugc_604_1_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 0hrep2-4p  0hrep2/ugc_604_4_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 0hrep3-4p  0hrep3/ugc_604_7_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c

./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 2hrep1-4p  2hrep1/ugc_604_2_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 2hrep2-4p  2hrep2/ugc_604_5_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 2hrep3-4p  2hrep3/ugc_604_8_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c

./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 6hrep1-4p  6hrep1/ugc_604_3_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 6hrep2-4p  6hrep2/ugc_604_6_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o 6hrep3-4p  6hrep3/ugc_604_9_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c

./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o IL4-4p  IL4/ugc_604_11_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer -m 10 -v 2 -p 10 -i -o IFN-4p  IFN/ugc_604_10_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c


#time ./PARalyzer 50G sample.ini-IGG-b 
#I identified a total of 4237592 reads mapping to 1072388 Unique genomic coordinates
#Making up 58618 groups
#Consisting of 21306 clusters