Rscript ~/code/spp/spp_package/run_spp.R -c=AL1G11460.t1_P_trichocarpa_Nisqually-1_DAPi712A10-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL1G11460.t1_P_trichocarpa_Nisqually-1_DAPi712A10-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL1G23550.t1_P_trichocarpa_Nisqually-1_DAPi712B03-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL1G23550.t1_P_trichocarpa_Nisqually-1_DAPi712B03-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL1G53260.t1_P_trichocarpa_Nisqually-1_DAPi712B01-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL1G53260.t1_P_trichocarpa_Nisqually-1_DAPi712B01-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL2G28980.t1_P_trichocarpa_Nisqually-1_DAPi712H11-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL2G28980.t1_P_trichocarpa_Nisqually-1_DAPi712H11-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL2G32420.t2_P_trichocarpa_Nisqually-1_DAPi712F10-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL2G32420.t2_P_trichocarpa_Nisqually-1_DAPi712F10-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL2G40550.t1_P_trichocarpa_Nisqually-1_DAPi712C11-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL2G40550.t1_P_trichocarpa_Nisqually-1_DAPi712C11-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL3G23910.t2_P_trichocarpa_Nisqually-1_DAPi712E07-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL3G23910.t2_P_trichocarpa_Nisqually-1_DAPi712E07-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL4G38490.t1_P_trichocarpa_Nisqually-1_DAPi712G08-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL4G38490.t1_P_trichocarpa_Nisqually-1_DAPi712G08-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL4G45550.t1_P_trichocarpa_Nisqually-1_DAPi712H06-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL4G45550.t1_P_trichocarpa_Nisqually-1_DAPi712H06-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL8G10650.t1_P_trichocarpa_Nisqually-1_DAPi712D09-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL8G10650.t1_P_trichocarpa_Nisqually-1_DAPi712D09-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AL8G13510.t2_P_trichocarpa_Nisqually-1_DAPi712B08-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AL8G13510.t2_P_trichocarpa_Nisqually-1_DAPi712B08-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G01060_P_trichocarpa_Nisqually-1_DAPi712H05-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G01060_P_trichocarpa_Nisqually-1_DAPi712H05-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G12260_P_trichocarpa_Nisqually-1_DAPi712C12-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G12260_P_trichocarpa_Nisqually-1_DAPi712C12-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G13260_P_trichocarpa_Nisqually-1_DAPi712E01-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G13260_P_trichocarpa_Nisqually-1_DAPi712E01-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G18330_P_trichocarpa_Nisqually-1_DAPi712G01-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G18330_P_trichocarpa_Nisqually-1_DAPi712G01-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G20910_P_trichocarpa_Nisqually-1_DAPi712B10-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G20910_P_trichocarpa_Nisqually-1_DAPi712B10-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G20980_P_trichocarpa_Nisqually-1_DAPi712E11-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G20980_P_trichocarpa_Nisqually-1_DAPi712E11-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G27730_P_trichocarpa_Nisqually-1_DAPi712C01-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G27730_P_trichocarpa_Nisqually-1_DAPi712C01-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G29160_P_trichocarpa_Nisqually-1_DAPi712B04-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G29160_P_trichocarpa_Nisqually-1_DAPi712B04-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G33240_P_trichocarpa_Nisqually-1_DAPi712F03-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G33240_P_trichocarpa_Nisqually-1_DAPi712F03-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G46768_P_trichocarpa_Nisqually-1_DAPi712G04-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G46768_P_trichocarpa_Nisqually-1_DAPi712G04-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G49480_P_trichocarpa_Nisqually-1_DAPi712A04-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G49480_P_trichocarpa_Nisqually-1_DAPi712A04-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G52880_P_trichocarpa_Nisqually-1_DAPi712E12-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G52880_P_trichocarpa_Nisqually-1_DAPi712E12-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G69180_P_trichocarpa_Nisqually-1_DAPi712G05-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G69180_P_trichocarpa_Nisqually-1_DAPi712G05-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G69690_P_trichocarpa_Nisqually-1_DAPi712C02-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G69690_P_trichocarpa_Nisqually-1_DAPi712C02-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G69780_P_trichocarpa_Nisqually-1_DAPi712A03-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G69780_P_trichocarpa_Nisqually-1_DAPi712A03-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G72740_P_trichocarpa_Nisqually-1_DAPi712G09-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G72740_P_trichocarpa_Nisqually-1_DAPi712G09-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G74480_P_trichocarpa_Nisqually-1_DAPi712D07-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G74480_P_trichocarpa_Nisqually-1_DAPi712D07-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G76420_P_trichocarpa_Nisqually-1_DAPi712C09-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G76420_P_trichocarpa_Nisqually-1_DAPi712C09-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G76880_P_trichocarpa_Nisqually-1_DAPi712F11-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G76880_P_trichocarpa_Nisqually-1_DAPi712F11-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G79580_P_trichocarpa_Nisqually-1_DAPi712B09-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G79580_P_trichocarpa_Nisqually-1_DAPi712B09-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT1G80840_P_trichocarpa_Nisqually-1_DAPi712G03-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT1G80840_P_trichocarpa_Nisqually-1_DAPi712G03-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G01060_P_trichocarpa_Nisqually-1_DAPi712F05-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G01060_P_trichocarpa_Nisqually-1_DAPi712F05-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G01930_P_trichocarpa_Nisqually-1_DAPi712D05-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G01930_P_trichocarpa_Nisqually-1_DAPi712D05-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G01940_P_trichocarpa_Nisqually-1_DAPi712G08-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G01940_P_trichocarpa_Nisqually-1_DAPi712G08-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G02820_P_trichocarpa_Nisqually-1_DAPi712F08-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G02820_P_trichocarpa_Nisqually-1_DAPi712F08-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G18550_P_trichocarpa_Nisqually-1_DAPi712E07-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G18550_P_trichocarpa_Nisqually-1_DAPi712E07-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G22430_P_trichocarpa_Nisqually-1_DAPi712H02-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G22430_P_trichocarpa_Nisqually-1_DAPi712H02-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G30250_P_trichocarpa_Nisqually-1_DAPi712H03-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G30250_P_trichocarpa_Nisqually-1_DAPi712H03-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G40620_P_trichocarpa_Nisqually-1_DAPi712B12-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G40620_P_trichocarpa_Nisqually-1_DAPi712B12-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G45420_P_trichocarpa_Nisqually-1_DAPi712F06-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G45420_P_trichocarpa_Nisqually-1_DAPi712F06-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G45480_P_trichocarpa_Nisqually-1_DAPi712F09-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G45480_P_trichocarpa_Nisqually-1_DAPi712F09-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G46270_P_trichocarpa_Nisqually-1_DAPi712H11-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G46270_P_trichocarpa_Nisqually-1_DAPi712H11-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT2G47070_P_trichocarpa_Nisqually-1_DAPi712H10-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT2G47070_P_trichocarpa_Nisqually-1_DAPi712H10-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G02940_P_trichocarpa_Nisqually-1_DAPi712H04-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G02940_P_trichocarpa_Nisqually-1_DAPi712H04-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G08500_P_trichocarpa_Nisqually-1_DAPi712B05-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G08500_P_trichocarpa_Nisqually-1_DAPi712B05-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G12250_P_trichocarpa_Nisqually-1_DAPi712A07-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G12250_P_trichocarpa_Nisqually-1_DAPi712A07-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G18990_P_trichocarpa_Nisqually-1_DAPi712D11-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G18990_P_trichocarpa_Nisqually-1_DAPi712D11-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G27010_P_trichocarpa_Nisqually-1_DAPi712C04-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G27010_P_trichocarpa_Nisqually-1_DAPi712C04-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G50060_P_trichocarpa_Nisqually-1_DAPi712G02-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G50060_P_trichocarpa_Nisqually-1_DAPi712G02-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G50260_P_trichocarpa_Nisqually-1_DAPi712D02-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G50260_P_trichocarpa_Nisqually-1_DAPi712D02-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G50410_P_trichocarpa_Nisqually-1_DAPi712H06-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G50410_P_trichocarpa_Nisqually-1_DAPi712H06-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G56400_P_trichocarpa_Nisqually-1_DAPi712B02-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G56400_P_trichocarpa_Nisqually-1_DAPi712B02-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G57920_P_trichocarpa_Nisqually-1_DAPi712D06-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G57920_P_trichocarpa_Nisqually-1_DAPi712D06-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G60530_P_trichocarpa_Nisqually-1_DAPi712E05-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT3G60530_P_trichocarpa_Nisqually-1_DAPi712E05-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT4G00730_P_trichocarpa_Nisqually-1_DAPi712C11-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT4G00730_P_trichocarpa_Nisqually-1_DAPi712C11-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT4G14770_P_trichocarpa_Nisqually-1_DAPi712F10-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT4G14770_P_trichocarpa_Nisqually-1_DAPi712F10-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT4G17980_P_trichocarpa_Nisqually-1_DAPi712E10-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT4G17980_P_trichocarpa_Nisqually-1_DAPi712E10-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT4G25470_P_trichocarpa_Nisqually-1_DAPi712B06-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT4G25470_P_trichocarpa_Nisqually-1_DAPi712B06-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT4G25480_P_trichocarpa_Nisqually-1_DAPi712F04-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT4G25480_P_trichocarpa_Nisqually-1_DAPi712F04-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT4G25490_P_trichocarpa_Nisqually-1_DAPi712A08-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT4G25490_P_trichocarpa_Nisqually-1_DAPi712A08-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT4G31800_P_trichocarpa_Nisqually-1_DAPi712F02-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT4G31800_P_trichocarpa_Nisqually-1_DAPi712F02-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G02320_P_trichocarpa_Nisqually-1_DAPi712G06-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G02320_P_trichocarpa_Nisqually-1_DAPi712G06-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G03150_P_trichocarpa_Nisqually-1_DAPi712D08-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G03150_P_trichocarpa_Nisqually-1_DAPi712D08-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G03790_P_trichocarpa_Nisqually-1_DAPi712C06-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G03790_P_trichocarpa_Nisqually-1_DAPi712C06-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G05550_P_trichocarpa_Nisqually-1_DAPi712A10-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G05550_P_trichocarpa_Nisqually-1_DAPi712A10-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G09410_P_trichocarpa_Nisqually-1_DAPi712G11-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G09410_P_trichocarpa_Nisqually-1_DAPi712G11-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G10030_P_trichocarpa_Nisqually-1_DAPi712A06-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G10030_P_trichocarpa_Nisqually-1_DAPi712A06-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G11260_P_trichocarpa_Nisqually-1_DAPi712D12-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G11260_P_trichocarpa_Nisqually-1_DAPi712D12-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G14960_P_trichocarpa_Nisqually-1_DAPi712E08-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G14960_P_trichocarpa_Nisqually-1_DAPi712E08-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G17300_P_trichocarpa_Nisqually-1_DAPi712H08-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G17300_P_trichocarpa_Nisqually-1_DAPi712H08-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G18560_P_trichocarpa_Nisqually-1_DAPi712H07-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G18560_P_trichocarpa_Nisqually-1_DAPi712H07-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G19790_P_trichocarpa_Nisqually-1_DAPi712G07-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G19790_P_trichocarpa_Nisqually-1_DAPi712G07-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G39760_P_trichocarpa_Nisqually-1_DAPi712A02-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G39760_P_trichocarpa_Nisqually-1_DAPi712A02-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G45300_P_trichocarpa_Nisqually-1_DAPi712G10-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G45300_P_trichocarpa_Nisqually-1_DAPi712G10-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G47390_P_trichocarpa_Nisqually-1_DAPi712F01-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G47390_P_trichocarpa_Nisqually-1_DAPi712F01-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G52830_P_trichocarpa_Nisqually-1_DAPi712F07-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G52830_P_trichocarpa_Nisqually-1_DAPi712F07-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G56110_P_trichocarpa_Nisqually-1_DAPi712E06-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G56110_P_trichocarpa_Nisqually-1_DAPi712E06-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G60130_P_trichocarpa_Nisqually-1_DAPi712C07-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G60130_P_trichocarpa_Nisqually-1_DAPi712C07-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G62020_P_trichocarpa_Nisqually-1_DAPi712E04-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G62020_P_trichocarpa_Nisqually-1_DAPi712E04-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G62470_P_trichocarpa_Nisqually-1_DAPi712C08-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G62470_P_trichocarpa_Nisqually-1_DAPi712C08-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G62940_P_trichocarpa_Nisqually-1_DAPi712A05-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G62940_P_trichocarpa_Nisqually-1_DAPi712A05-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G64750_P_trichocarpa_Nisqually-1_DAPi712E03-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G64750_P_trichocarpa_Nisqually-1_DAPi712E03-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G65410_P_trichocarpa_Nisqually-1_DAPi712D03-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G65410_P_trichocarpa_Nisqually-1_DAPi712D03-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G67300_P_trichocarpa_Nisqually-1_DAPi712B01-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=AT5G67300_P_trichocarpa_Nisqually-1_DAPi712B01-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0001s0116.1_P_trichocarpa_Nisqually-1_DAPi712C10-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0001s0116.1_P_trichocarpa_Nisqually-1_DAPi712C10-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0001s1194.1_P_trichocarpa_Nisqually-1_DAPi712D03-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0001s1194.1_P_trichocarpa_Nisqually-1_DAPi712D03-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0001s3581.1.p_P_trichocarpa_Nisqually-1_DAPi712D01-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0001s3581.1.p_P_trichocarpa_Nisqually-1_DAPi712D01-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0002s1646.1_P_trichocarpa_Nisqually-1_DAPi712C12-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0002s1646.1_P_trichocarpa_Nisqually-1_DAPi712C12-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0002s1959.1_P_trichocarpa_Nisqually-1_DAPi712H10-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0002s1959.1_P_trichocarpa_Nisqually-1_DAPi712H10-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0002s2670.1_P_trichocarpa_Nisqually-1_DAPi712E11-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0002s2670.1_P_trichocarpa_Nisqually-1_DAPi712E11-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0003s1161.1.p_P_trichocarpa_Nisqually-1_DAPi712G07-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0003s1161.1.p_P_trichocarpa_Nisqually-1_DAPi712G07-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0004s2291.1_P_trichocarpa_Nisqually-1_DAPi712A09-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0004s2291.1_P_trichocarpa_Nisqually-1_DAPi712A09-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0004s2898.1.p_P_trichocarpa_Nisqually-1_DAPi712B07-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0004s2898.1.p_P_trichocarpa_Nisqually-1_DAPi712B07-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0008s0039.1_P_trichocarpa_Nisqually-1_DAPi712F09-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0008s0039.1_P_trichocarpa_Nisqually-1_DAPi712F09-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Carub.0008s0285.1_P_trichocarpa_Nisqually-1_DAPi712D08-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Carub.0008s0285.1_P_trichocarpa_Nisqually-1_DAPi712D08-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A01-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A01-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A01-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A01-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A12-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A12-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A12-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A12-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H01-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H01-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H01-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H01-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H12-ORGi5033-96P220.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H12-ORGi5033-96P220.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H12-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H12-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os01g17260.2_P_trichocarpa_Nisqually-1_DAPi712H07-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os01g17260.2_P_trichocarpa_Nisqually-1_DAPi712H07-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os01g18240.1_P_trichocarpa_Nisqually-1_DAPi712G04-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os01g18240.1_P_trichocarpa_Nisqually-1_DAPi712G04-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os01g46970.1_P_trichocarpa_Nisqually-1_DAPi712C07-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os01g46970.1_P_trichocarpa_Nisqually-1_DAPi712C07-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os01g51154.1_P_trichocarpa_Nisqually-1_DAPi712A11-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os01g51154.1_P_trichocarpa_Nisqually-1_DAPi712A11-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os02g33430.1_P_trichocarpa_Nisqually-1_DAPi712D05-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os02g33430.1_P_trichocarpa_Nisqually-1_DAPi712D05-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os02g42970.1_P_trichocarpa_Nisqually-1_DAPi712E03-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os02g42970.1_P_trichocarpa_Nisqually-1_DAPi712E03-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os03g21800.1_P_trichocarpa_Nisqually-1_DAPi712B09-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os03g21800.1_P_trichocarpa_Nisqually-1_DAPi712B09-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os06g07030.1_P_trichocarpa_Nisqually-1_DAPi712E01-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os06g07030.1_P_trichocarpa_Nisqually-1_DAPi712E01-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os08g06110.3_P_trichocarpa_Nisqually-1_DAPi712D10-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os08g06110.3_P_trichocarpa_Nisqually-1_DAPi712D10-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os08g37970.1_P_trichocarpa_Nisqually-1_DAPi712A06-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os08g37970.1_P_trichocarpa_Nisqually-1_DAPi712A06-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os09g25060.1_P_trichocarpa_Nisqually-1_DAPi712F11-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os09g25060.1_P_trichocarpa_Nisqually-1_DAPi712F11-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os10g26500.1_P_trichocarpa_Nisqually-1_DAPi712D12-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os10g26500.1_P_trichocarpa_Nisqually-1_DAPi712D12-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=LOC_Os10g41200.1_P_trichocarpa_Nisqually-1_DAPi712G09-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=LOC_Os10g41200.1_P_trichocarpa_Nisqually-1_DAPi712G09-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc01g095460.3.1_P_trichocarpa_Nisqually-1_DAPi712D07-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc01g095460.3.1_P_trichocarpa_Nisqually-1_DAPi712D07-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc01g102340.3.1_P_trichocarpa_Nisqually-1_DAPi712H04-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc01g102340.3.1_P_trichocarpa_Nisqually-1_DAPi712H04-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc03g116890.3.1_P_trichocarpa_Nisqually-1_DAPi712G11-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc03g116890.3.1_P_trichocarpa_Nisqually-1_DAPi712G11-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc04g078640.3.1_P_trichocarpa_Nisqually-1_DAPi712F01-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc04g078640.3.1_P_trichocarpa_Nisqually-1_DAPi712F01-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc05g007180.3.1_P_trichocarpa_Nisqually-1_DAPi712E12-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc05g007180.3.1_P_trichocarpa_Nisqually-1_DAPi712E12-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc06g048630.3.1_P_trichocarpa_Nisqually-1_DAPi712C09-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc06g048630.3.1_P_trichocarpa_Nisqually-1_DAPi712C09-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc07g040920.2.1_P_trichocarpa_Nisqually-1_DAPi712B11-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc07g040920.2.1_P_trichocarpa_Nisqually-1_DAPi712B11-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc08g068320.3.1_P_trichocarpa_Nisqually-1_DAPi712C04-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc08g068320.3.1_P_trichocarpa_Nisqually-1_DAPi712C04-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc08g078340.3.1_P_trichocarpa_Nisqually-1_DAPi712H09-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc08g078340.3.1_P_trichocarpa_Nisqually-1_DAPi712H09-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc08g079120.3.1_P_trichocarpa_Nisqually-1_DAPi712F03-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc08g079120.3.1_P_trichocarpa_Nisqually-1_DAPi712F03-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc10g005080.3.1_P_trichocarpa_Nisqually-1_DAPi712E10-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc10g005080.3.1_P_trichocarpa_Nisqually-1_DAPi712E10-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=Solyc11g064950.3.1_P_trichocarpa_Nisqually-1_DAPi712A08-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=Solyc11g064950.3.1_P_trichocarpa_Nisqually-1_DAPi712A08-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013586407.1_P_trichocarpa_Nisqually-1_DAPi712F07-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013586407.1_P_trichocarpa_Nisqually-1_DAPi712F07-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013587350.1_P_trichocarpa_Nisqually-1_DAPi712B10-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013587350.1_P_trichocarpa_Nisqually-1_DAPi712B10-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013587997.1_P_trichocarpa_Nisqually-1_DAPi712D11-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013587997.1_P_trichocarpa_Nisqually-1_DAPi712D11-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013589913.1_P_trichocarpa_Nisqually-1_DAPi712G10-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013589913.1_P_trichocarpa_Nisqually-1_DAPi712G10-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013589953.1_P_trichocarpa_Nisqually-1_DAPi712B12-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013589953.1_P_trichocarpa_Nisqually-1_DAPi712B12-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013602769.1_P_trichocarpa_Nisqually-1_DAPi712C03-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013602769.1_P_trichocarpa_Nisqually-1_DAPi712C03-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013609718.1_P_trichocarpa_Nisqually-1_DAPi712G12-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013609718.1_P_trichocarpa_Nisqually-1_DAPi712G12-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013613838.1_P_trichocarpa_Nisqually-1_DAPi712C08-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013613838.1_P_trichocarpa_Nisqually-1_DAPi712C08-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013615900.1_P_trichocarpa_Nisqually-1_DAPi712E09-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013615900.1_P_trichocarpa_Nisqually-1_DAPi712E09-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013629448.1_P_trichocarpa_Nisqually-1_DAPi712H03-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013629448.1_P_trichocarpa_Nisqually-1_DAPi712H03-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013631386.1_P_trichocarpa_Nisqually-1_DAPi712A07-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013631386.1_P_trichocarpa_Nisqually-1_DAPi712A07-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013631649.1_P_trichocarpa_Nisqually-1_DAPi712B05-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013631649.1_P_trichocarpa_Nisqually-1_DAPi712B05-ORGi5033-96P247.1x36mers.QC
Rscript ~/code/spp/spp_package/run_spp.R -c=XP_013634112.1_P_trichocarpa_Nisqually-1_DAPi712H08-ORGi5033-96P247.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=XP_013634112.1_P_trichocarpa_Nisqually-1_DAPi712H08-ORGi5033-96P247.1x36mers.QC