./saet [-options] refLength - expected length of sequenced (or enriched) region. Example: 4,600,000 for E.Coli 4.6Mb genome or 30,000,000 for Whole Human Transcriptome chipseq: 30000 genes * 200 nt peak (* 30000 200) 6000000 -fixdir dir Output spectrum and fixed reads into "dir" directory (Default "fixed"). -numcores p If multi-threading is supported then include this option to run the code in p parallel threads. -qvupdate reczko@estia:/data/images/proton/DKlab/mr/parclip/raw/saet$ /data/results/tools/solid/saet/saet ../IL4/ugc_604_11_F3.csfasta ../IL4/ugc_604_11_F3.QV.qual 3000000 -fixdir IL4 -qvupdate SOLiD(TM) Accuracy Enhancer Tool (SAET) v.2.2 Copyright (2009) by Life Technologies ********************************************* reczko@estia:/data/images/proton/DKlab/mr/parclip/raw/saet$ /data/results/tools/solid/saet/saet ../IFN/ugc_604_10_F3.csfasta ../IFN/ugc_604_10_F3.QV.qual 2000000 -fixdir IFN -qvupdate SOLiD(TM) Accuracy Enhancer Tool (SAET) v.2.2 Copyright (2009) by Life Technologies ********************************************* reczko@estia:/data/images/proton/DKlab/mr/parclip/raw/saet$ reczko@estia:/data/images/proton/DKlab/mr/parclip/raw/saet$ reczko@estia:/data/images/proton/DKlab/mr/parclip/raw/saet$ /data/results/tools/solid/saet/saet ../IFN/ugc_604_10_F3.csfasta ../IFN/ugc_604_10_F3.QV.qual 2500000 -fixdir IFNb -qvupdate SOLiD(TM) Accuracy Enhancer Tool (SAET) v.2.2 Copyright (2009) by Life Technologies ********************************************* reczko@estia:/data/images/proton/DKlab/mr/parclip/raw/saet$ /data/results/tools/solid/saet/saet ../IFN/ugc_604_10_F3.csfasta ../IFN/ugc_604_10_F3.QV.qual 3000000 -fixdir IFN -qvupdate SOLiD(TM) Accuracy Enhancer Tool (SAET) v.2.2 Copyright (2009) by Life Technologies ********************************************* Segmentation fault /data/results/tools/solid/saet/saet ../IGG/ugc_604_12_F3.csfasta ../IGG/ugc_604_12_F3.QV.qual 2000000 -fixdir IGG -qvupdate SOLiD(TM) Accuracy Enhancer Tool (SAET) v.2.2 Copyright (2009) by Life Technologies ********************************************* /data/results/tools/solid/saet/saet 2000000 -fixdir -qvupdate /data/results/tools/solid/saet/saet ../0hrep1/ugc_604_1_F3.csfasta ../0hrep1/ugc_604_1_F3.QV.qual 2000000 -fixdir 0hrep1 -qvupdate /data/results/tools/solid/saet/saet ../0hrep2/ugc_604_4_F3.csfasta ../0hrep2/ugc_604_4_F3.QV.qual 2000000 -fixdir 0hrep2 -qvupdate /data/results/tools/solid/saet/saet ../0hrep3/ugc_604_7_F3.csfasta ../0hrep3/ugc_604_7_F3.QV.qual 2000000 -fixdir 0hrep3 -qvupdate /data/results/tools/solid/saet/saet ../2hrep1/ugc_604_2_F3.csfasta ../2hrep1/ugc_604_2_F3.QV.qual 2000000 -fixdir 2hrep1 -qvupdate /data/results/tools/solid/saet/saet ../2hrep2/ugc_604_5_F3.csfasta ../2hrep2/ugc_604_5_F3.QV.qual 2000000 -fixdir 2hrep2 -qvupdate /data/results/tools/solid/saet/saet ../2hrep3/ugc_604_8_F3.csfasta ../2hrep3/ugc_604_8_F3.QV.qual 2000000 -fixdir 2hrep3 -qvupdate /data/results/tools/solid/saet/saet ../6hrep1/ugc_604_3_F3.csfasta ../6hrep1/ugc_604_3_F3.QV.qual 2000000 -fixdir 6hrep1 -qvupdate /data/results/tools/solid/saet/saet ../6hrep2/ugc_604_6_F3.csfasta ../6hrep2/ugc_604_6_F3.QV.qual 2000000 -fixdir 6hrep2 -qvupdate /data/results/tools/solid/saet/saet ../6hrep3/ugc_604_9_F3.csfasta ../6hrep3/ugc_604_9_F3.QV.qual 2000000 -fixdir 6hrep3 -qvupdate reczko@max:/data/images/proton/DKlab/mr/parclip/raw/saet$ /data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o IL4saet1 -f IL4/ugc_604_11_F3.csfasta -g IL4/ugc_604_11_F3.QV.qual Type of Input - F Polyclonal Analysis - y Min count for Polyclonal Analysis - 1 Min QV for Polyclonal Analysis - 25 Error Analysis - y Max count permitted errors - 3 Max QV to consider an error - 10 Removal of reads with negative QV score - n Truncation is off - n Quality Value analysis is on - y Output QV files - y Starting Anaysis - Fragment cat IL4saet1_T_F3.csfasta | /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/collapseFA.pl > IL4saet1_T_F3.csfasta.coll /data/images/proton/DKlab/mr/parclip/raw/SeqTrimMap4Paralyzer -m 10 -l 18 -v 2 -p 10 -i -o IL4F-s1 IL4saet1_T_F3.csfasta.coll /data/results/reference/mmu/mm9/bowtie1/mm9c reczko@max:/data/images/proton/DKlab/mr/parclip/raw/saet$ /data/images/proton/DKlab/mr/parclip/raw/SeqTrimMap4Paralyzer -m 10 -l 18 -v 2 -p 10 -i -o IL4-s1 IL4/ugc_604_11_F3.csfasta /data/results/reference/mmu/mm9/bowtie1/mm9c reczko@max:/data/images/proton/DKlab/mr/parclip/raw/saet$ /data/images/proton/DKlab/mr/parclip/raw/SeqTrimMap4Paralyzer -k -m 10 -l 18 -v 2 -p 10 -i -o IL4-s1k IL4/ugc_604_11_F3.csfasta /data/results/reference/mmu/mm9/bowtie1/mm9c ./SeqTrimMap4Paralyzer_bt0.12 -k -m 10 -l 18 -v 2 -p 10 -i -o IL4-s1k-bt0.12 IL4/ugc_604_11_F3.csfasta /data/results/reference/mmu/mm9/bowtie1/mm9c