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# Processing Histone centric data
bedops --everything H3K4me1_filtered_peaks.bed H3K27ac_filtered_peaks.bed | bedops -m --range -1 - > Histone_putative_enhancers.bed
./rpkm.py --peaks Histone_putative_enhancers.bed --experiments h3k27ac_list.csv -f Histone_h3k27ac --minimum 1
./rpkm.py --peaks Histone_putative_enhancers.bed --experiments h3k4me1_list.csv -f Histone_h3k4me1 --minimum 1
./rpkm.py --peaks Histone_putative_enhancers.bed --experiments putative_histone_enhancers.csv -f Histone_pe --minimum 0
awk -F\, '{print $0 "\tHE_" NR}' Histone_pe_filtered_peaks.bed > t
mv t Histone_pe_filtered_peaks.bed
grep chrom Histone_pe_filtered_peaks.tsv | awk -F\, '{print $0 "\tname"}' > t
grep -v chrom Histone_pe_filtered_peaks.tsv | awk -F\, '{print $0 "\tHE_" NR}' >> t
mv t Histone_pe_filtered_peaks.tsv
# Acutal Processing
python histone_enhancer_plots.py
# Getting surround 1kb
python extend_histone_1kb.py -e ES_D0_Histone_enhancers.bed -o ES_D0_Histone_enhancers_1kb
python extend_histone_1kb.py -e ES_D2_Histone_enhancers.bed -o ES_D2_Histone_enhancers_1kb
python extend_histone_1kb.py -e ES_D5_Histone_enhancers.bed -o ES_D5_Histone_enhancers_1kb
python extend_histone_1kb.py -e ES_D7_Histone_enhancers.bed -o ES_D7_Histone_enhancers_1kb
python extend_histone_1kb.py -e ES_D10_Histone_enhancers.bed -o ES_D10_Histone_enhancers_1kb
# Meme processing
#!/bin/bash
#SBATCH --job-name=fasta_processing
#SBATCH --partition=super
#SBATCH --nodes=2
#SBATCH --ntasks=64
#SBATCH --time=0-36:00:00
#SBATCH --output=fasta_processing.%j.out
#SBATCH --error=fasta_processing.%j.err
#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
#SBATCH --mail-type=ALL
# Fasta file processing
module load bedtools
bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D0_Histone_enhancers_1kb.bed -fo ES_D0_Histone_enhancers_1kb.fasta -name
bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D2_Histone_enhancers_1kb.bed -fo ES_D2_Histone_enhancers_1kb.fasta -name
bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D5_Histone_enhancers_1kb.bed -fo ES_D5_Histone_enhancers_1kb.fasta -name
bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D7_Histone_enhancers_1kb.bed -fo ES_D7_Histone_enhancers_1kb.fasta -name
bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D10_Histone_enhancers_1kb.bed -fo ES_D10_Histone_enhancers_1kb.fasta -name
# Meme processing
#!/bin/bash
#SBATCH --job-name=meme_test
#SBATCH --partition=super
#SBATCH --nodes=2
#SBATCH --ntasks=64
#SBATCH --time=0-36:00:00
#SBATCH --output=meme_test.%j.out
#SBATCH --error=meme_test.%j.err
#SBATCH --mail-user=venkat.malladi@utsouthwestern.edu
#SBATCH --mail-type=ALL
module load meme/4.11.0-intel-mvapich2
#!/bin/bash
#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
# Use super partition
#SBATCH --partition=super
# Use 2 nodes
#SBATCH -N 2
# Total of 96 tasks
#SBATCH -n 96
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 -nmeme 1000 -norand -spamo-skip -fimo-skip -ccut 500 -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 -nmeme 1000 -norand -spamo-skip -fimo-skip -ccut 500 -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 -nmeme 1000 -norand -spamo-skip -fimo-skip -ccut 500 -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_D5_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 -nmeme 1000 -norand -spamo-skip -fimo-skip -ccut 500 -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 -nmeme 1000 -norand -spamo-skip -fimo-skip -ccut 500 -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
meme -p 96 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 200000000 -revcomp ES_D0_Histone_enhancers_1kb.fasta -o MEME_op_ES_D0_Histone_enhancers_1kb_zoops
meme -p 96 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 200000000 -revcomp ES_D2_Histone_enhancers_1kb.fasta -o MEME_op_ES_D2_Histone_enhancers_1kb_zoops
meme -p 96 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 200000000 -revcomp ES_D5_Histone_enhancers_1kb.fasta -o MEME_op_ES_D5_Histone_enhancers_1kb_zoops
meme -p 96 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 200000000 -revcomp ES_D7_Histone_enhancers_1kb.fasta -o MEME_op_ES_D7_Histone_enhancers_1kb_zoops
meme -p 96 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 200000000 -revcomp 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