Histone centered processing.

histone_centered_processing.sh

@@ -66,10 +66,11 @@ module load meme/4.11.0-intel-mvapich2
 
 #!/bin/bash
 
-#SBATCH --job-name=meme_test
-#SBATCH --output=meme_test.%j.out
-#SBATCH --error=meme_test.%j.err
+#SBATCH --job-name=meme_histone_test
+#SBATCH --output=meme_histone_test.%j.out
+#SBATCH --error=meme_histone_test.%j.err
 #SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
+#SBATCH --mail-type=ALL
 # Use super partition
 #SBATCH --partition=super
 
@@ -79,11 +80,30 @@ module load meme/4.11.0-intel-mvapich2
 # Total of 96 tasks
 #SBATCH -n 96
 
-#SBATCH -t 1:0:0
 
 module add meme/4.11.1-gcc-openmpi
-meme-chip -meme-p 96 -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -db /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016.meme ES_D0_Histone_enhancers_1kb.fasta -o MEME_op_ES_D0_Histone_enhancers_1kb_zoops
-meme -meme-p -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -revcomp ES_D2_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D2_H3K27ac_1kb_zoops
-meme -meme-p -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -revcomp ES_D5_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D5_H3K27ac_1kb_zoops
-meme -meme-p -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -revcomp ES_D7_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D7_H3K27ac_1kb_zoops
-meme -meme-p -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -revcomp ES_D10_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D10_H3K27ac_1kb_zoops
+meme-chip -meme-p 96 -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -spamo-skip -fimo-skip -db /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme ES_D0_Histone_enhancers_1kb.fasta -o MEME_op_ES_D0_Histone_enhancers_1kb_zoops
+meme-chip -meme-p 96 -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -spamo-skip -fimo-skip -db /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme ES_D2_Histone_enhancers_1kb.fasta -o MEME_op_ES_D2_Histone_enhancers_1kb_zoops
+meme-chip -meme-p 96 -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -spamo-skip -fimo-skip -db /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme ES_D5_Histone_enhancers_1kb.fasta -o MEME_op_ES_D5Histone_enhancers_1kb_zoops
+meme-chip -meme-p 96 -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -spamo-skip -fimo-skip -db /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme ES_D7_Histone_enhancers_1kb.fasta -o MEME_op_ES_D7_Histone_enhancers_1kb_zoops
+meme-chip -meme-p 96 -dna -meme-mod zoops -meme-nmotifs 15 -meme-minw 8 -meme-maxw 15 -meme-maxsize 20000000 -spamo-skip -fimo-skip -db /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme ES_D10__Histone_enhancers_1kb.fasta -o MEME_op_ES_D10_Histone_enhancers_1kb_zoops
+
+
+#!/bin/bash
+
+#SBATCH --job-name=tomtom_test_histone
+#SBATCH --output=tomtom_test_gro.%j.out
+#SBATCH --error=tomtom_test_gro.%j.err
+#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
+# Use super partition
+#SBATCH --partition=super
+
+# Use 2 nodes
+#SBATCH -N 2
+
+module add meme/4.11.1-gcc-openmpi
+tomtom -evalue -thresh 10 -o tomtom_op_ES_D0_Histone_enhancers_1kb /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/Motif/MEME_op_ES_D0_Histone_enhancers_1kb_zoops/meme_out/meme.txt  /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme
+tomtom -evalue -thresh 10 -o tomtom_op_ES_D10_Histone_enhancers_1kb /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/Motif/MEME_op_ES_D10_Histone_enhancers_1kb_zoops/meme_out/meme.txt  /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme
+tomtom -evalue -thresh 10 -o tomtom_op_ES_D2_Histone_enhancers_1kb /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/Motif/MEME_op_ES_D2_Histone_enhancers_1kb_zoops/meme_out/meme.txt  /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme
+tomtom -evalue -thresh 10 -o tomtom_op_ES_D5_Histone_enhancers_1kb /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/Motif/MEME_op_ES_D5_Histone_enhancers_1kb_zoops/meme_out/meme.txt  /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme
+tomtom -evalue -thresh 10 -o tomtom_op_ES_D7_Histone_enhancers_1kb /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/Motif/MEME_op_ES_D7_Histone_enhancers_1kb_zoops/meme_out/meme.txt  /project/GCRB/Lee_Lab/shared/For_CBs/databases/meme_motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme