cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_219-11-TomD_Lynch100514Set1.read1.fastq.gz Sample_219-11-TomD_Lynch100514Set1.read2.fastq.gz Sample_219-11-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_219-11-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_219-11-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_219-11-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_223-TomD_Lynch100514Set1.read1.fastq.gz Sample_223-TomD_Lynch100514Set1.read2.fastq.gz Sample_223-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_223-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_223-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_223-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_227-TomD_Lynch100514Set1.read1.fastq.gz Sample_227-TomD_Lynch100514Set1.read2.fastq.gz Sample_227-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_227-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_227-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_227-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_23Maymale13515-TomD_Lynch100514Set1.read1.fastq.gz Sample_23Maymale13515-TomD_Lynch100514Set1.read2.fastq.gz Sample_23Maymale13515-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_23Maymale13515-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_23Maymale13515-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_23Maymale13515-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_5JunePE13515-TomD_Lynch100514Set1.read1.fastq.gz Sample_5JunePE13515-TomD_Lynch100514Set1.read2.fastq.gz Sample_5JunePE13515-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_5JunePE13515-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_5JunePE13515-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_5JunePE13515-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_BM4-1-TomD_Lynch100514Set1.read1.fastq.gz Sample_BM4-1-TomD_Lynch100514Set1.read2.fastq.gz Sample_BM4-1-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_BM4-1-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_BM4-1-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_BM4-1-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_K12-TomD_Lynch100514Set1.read1.fastq.gz Sample_K12-TomD_Lynch100514Set1.read2.fastq.gz Sample_K12-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_K12-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_K12-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_K12-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_M-TomD_Lynch100514Set1.read1.fastq.gz Sample_M-TomD_Lynch100514Set1.read2.fastq.gz Sample_M-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_M-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_M-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_M-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_PB-TomD_Lynch100514Set1.read1.fastq.gz Sample_PB-TomD_Lynch100514Set1.read2.fastq.gz Sample_PB-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_PB-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_PB-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_PB-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_dec-TomD_Lynch100514Set1.read1.fastq.gz Sample_dec-TomD_Lynch100514Set1.read2.fastq.gz Sample_dec-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_dec-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_dec-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_dec-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_ovt-TomD_Lynch100514Set1.read1.fastq.gz Sample_ovt-TomD_Lynch100514Set1.read2.fastq.gz Sample_ovt-TomD_Lynch100514Set1.read1.paired.fastq.gz Sample_ovt-TomD_Lynch100514Set1.read1.unpaired.fastq.gz Sample_ovt-TomD_Lynch100514Set1.read2.paired.fastq.gz Sample_ovt-TomD_Lynch100514Set1.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_209-TomD_Lynch100514Set2.read1.fastq.gz Sample_209-TomD_Lynch100514Set2.read2.fastq.gz Sample_209-TomD_Lynch100514Set2.read1.paired.fastq.gz Sample_209-TomD_Lynch100514Set2.read1.unpaired.fastq.gz Sample_209-TomD_Lynch100514Set2.read2.paired.fastq.gz Sample_209-TomD_Lynch100514Set2.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_858-TomD_Lynch100514Set2.read1.fastq.gz Sample_858-TomD_Lynch100514Set2.read2.fastq.gz Sample_858-TomD_Lynch100514Set2.read1.paired.fastq.gz Sample_858-TomD_Lynch100514Set2.read1.unpaired.fastq.gz Sample_858-TomD_Lynch100514Set2.read2.paired.fastq.gz Sample_858-TomD_Lynch100514Set2.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_9June1A13515-TomD_Lynch100514Set2.read1.fastq.gz Sample_9June1A13515-TomD_Lynch100514Set2.read2.fastq.gz Sample_9June1A13515-TomD_Lynch100514Set2.read1.paired.fastq.gz Sample_9June1A13515-TomD_Lynch100514Set2.read1.unpaired.fastq.gz Sample_9June1A13515-TomD_Lynch100514Set2.read2.paired.fastq.gz Sample_9June1A13515-TomD_Lynch100514Set2.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_MA-TomD_Lynch100514Set2.read1.fastq.gz Sample_MA-TomD_Lynch100514Set2.read2.fastq.gz Sample_MA-TomD_Lynch100514Set2.read1.paired.fastq.gz Sample_MA-TomD_Lynch100514Set2.read1.unpaired.fastq.gz Sample_MA-TomD_Lynch100514Set2.read2.paired.fastq.gz Sample_MA-TomD_Lynch100514Set2.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_PO-TomD_Lynch100514Set2.read1.fastq.gz Sample_PO-TomD_Lynch100514Set2.read2.fastq.gz Sample_PO-TomD_Lynch100514Set2.read1.paired.fastq.gz Sample_PO-TomD_Lynch100514Set2.read1.unpaired.fastq.gz Sample_PO-TomD_Lynch100514Set2.read2.paired.fastq.gz Sample_PO-TomD_Lynch100514Set2.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_PbU4-1-TomD_Lynch100514Set2.read1.fastq.gz Sample_PbU4-1-TomD_Lynch100514Set2.read2.fastq.gz Sample_PbU4-1-TomD_Lynch100514Set2.read1.paired.fastq.gz Sample_PbU4-1-TomD_Lynch100514Set2.read1.unpaired.fastq.gz Sample_PbU4-1-TomD_Lynch100514Set2.read2.paired.fastq.gz Sample_PbU4-1-TomD_Lynch100514Set2.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_Psonn-TomD_Lynch100514Set2.read1.fastq.gz Sample_Psonn-TomD_Lynch100514Set2.read2.fastq.gz Sample_Psonn-TomD_Lynch100514Set2.read1.paired.fastq.gz Sample_Psonn-TomD_Lynch100514Set2.read1.unpaired.fastq.gz Sample_Psonn-TomD_Lynch100514Set2.read2.paired.fastq.gz Sample_Psonn-TomD_Lynch100514Set2.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_TE2-16-TomD_Lynch100514Set2.read1.fastq.gz Sample_TE2-16-TomD_Lynch100514Set2.read2.fastq.gz Sample_TE2-16-TomD_Lynch100514Set2.read1.paired.fastq.gz Sample_TE2-16-TomD_Lynch100514Set2.read1.unpaired.fastq.gz Sample_TE2-16-TomD_Lynch100514Set2.read2.paired.fastq.gz Sample_TE2-16-TomD_Lynch100514Set2.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_10V-TomD_LynchAB_RP4.read1.fastq.gz Sample_10V-TomD_LynchAB_RP4.read2.fastq.gz Sample_10V-TomD_LynchAB_RP4.read1.paired.fastq.gz Sample_10V-TomD_LynchAB_RP4.read1.unpaired.fastq.gz Sample_10V-TomD_LynchAB_RP4.read2.paired.fastq.gz Sample_10V-TomD_LynchAB_RP4.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_12V-TomD_LynchAB_RP4.read1.fastq.gz Sample_12V-TomD_LynchAB_RP4.read2.fastq.gz Sample_12V-TomD_LynchAB_RP4.read1.paired.fastq.gz Sample_12V-TomD_LynchAB_RP4.read1.unpaired.fastq.gz Sample_12V-TomD_LynchAB_RP4.read2.paired.fastq.gz Sample_12V-TomD_LynchAB_RP4.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_1D1-TomD_LynchAB_RP4.read1.fastq.gz Sample_1D1-TomD_LynchAB_RP4.read2.fastq.gz Sample_1D1-TomD_LynchAB_RP4.read1.paired.fastq.gz Sample_1D1-TomD_LynchAB_RP4.read1.unpaired.fastq.gz Sample_1D1-TomD_LynchAB_RP4.read2.paired.fastq.gz Sample_1D1-TomD_LynchAB_RP4.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_227-TomD_LynchAB_RP4.read1.fastq.gz Sample_227-TomD_LynchAB_RP4.read2.fastq.gz Sample_227-TomD_LynchAB_RP4.read1.paired.fastq.gz Sample_227-TomD_LynchAB_RP4.read1.unpaired.fastq.gz Sample_227-TomD_LynchAB_RP4.read2.paired.fastq.gz Sample_227-TomD_LynchAB_RP4.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_4D_2_14_16_12-TomD_LynchAB_RP4.read1.fastq.gz Sample_4D_2_14_16_12-TomD_LynchAB_RP4.read2.fastq.gz Sample_4D_2_14_16_12-TomD_LynchAB_RP4.read1.paired.fastq.gz Sample_4D_2_14_16_12-TomD_LynchAB_RP4.read1.unpaired.fastq.gz Sample_4D_2_14_16_12-TomD_LynchAB_RP4.read2.paired.fastq.gz Sample_4D_2_14_16_12-TomD_LynchAB_RP4.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_4D_2_24_16_12-TomD_LynchAB_RP4.read1.fastq.gz Sample_4D_2_24_16_12-TomD_LynchAB_RP4.read2.fastq.gz Sample_4D_2_24_16_12-TomD_LynchAB_RP4.read1.paired.fastq.gz Sample_4D_2_24_16_12-TomD_LynchAB_RP4.read1.unpaired.fastq.gz Sample_4D_2_24_16_12-TomD_LynchAB_RP4.read2.paired.fastq.gz Sample_4D_2_24_16_12-TomD_LynchAB_RP4.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_A39-TomD_LynchAB_RP4.read1.fastq.gz Sample_A39-TomD_LynchAB_RP4.read2.fastq.gz Sample_A39-TomD_LynchAB_RP4.read1.paired.fastq.gz Sample_A39-TomD_LynchAB_RP4.read1.unpaired.fastq.gz Sample_A39-TomD_LynchAB_RP4.read2.paired.fastq.gz Sample_A39-TomD_LynchAB_RP4.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-05-27-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE Sample_K412-TomD_LynchAB_RP4.read1.fastq.gz Sample_K412-TomD_LynchAB_RP4.read2.fastq.gz Sample_K412-TomD_LynchAB_RP4.read1.paired.fastq.gz Sample_K412-TomD_LynchAB_RP4.read1.unpaired.fastq.gz Sample_K412-TomD_LynchAB_RP4.read2.paired.fastq.gz Sample_K412-TomD_LynchAB_RP4.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &