From 9c3858b46268715feb1ac873b19dbba1fa7a13e4 Mon Sep 17 00:00:00 2001 From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu> Date: Mon, 10 Apr 2017 10:37:12 -0500 Subject: [PATCH] Histone centered processing. --- histone_centered_processing.sh | 38 ++++++++++++++++++++++++++-------- 1 file changed, 29 insertions(+), 9 deletions(-) diff --git a/histone_centered_processing.sh b/histone_centered_processing.sh index 131110f..ccff026 100644 --- a/histone_centered_processing.sh +++ b/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 -- GitLab