From 7a9a34d2d68c1ea3e3f0ebce13ff9402bd6e1b6d Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Tue, 21 Feb 2017 12:58:50 -0600
Subject: [PATCH] Update histone centered processing.
---
histone_centered_processing.sh | 42 ++++++++--------------------------
1 file changed, 10 insertions(+), 32 deletions(-)
diff --git a/histone_centered_processing.sh b/histone_centered_processing.sh
index ade54ac..b197ec0 100644
--- a/histone_centered_processing.sh
+++ b/histone_centered_processing.sh
@@ -2,41 +2,19 @@
bedops --everything H3K4me1_filtered_peaks.bed H3K27ac_filtered_peaks.bed | bedops -m --range -1 - > Histone_putative_enhancers.bed
+
# RPKM Filtering
# Get RPKM
+./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
-# Acutal Processing
-./define_histone_window.py --enhancers H3K27ac_filtered_peaks.bed
-./rpkm_name.py --peaks enhancers_renamed.bed --experiments h3k27ac_list.csv -f H3K27ac
-
-
-# histone Processing
-bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D0_H3K27ac_filtered_peaks.bed -fo ES_D0_H3K27ac_filtered_peaks.fasta -name
-bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D2_H3K27ac_filtered_peaks.bed -fo ES_D2_H3K27ac_filtered_peaks.fasta -name
-bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D5_H3K27ac_filtered_peaks.bed -fo ES_D5_H3K27ac_filtered_peaks.fasta -name
-bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D7_H3K27ac_filtered_peaks.bed -fo ES_D7_H3K27ac_filtered_peaks.fasta -name
-bedtools getfasta -fi /project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bed ES_D10_H3K27ac_filtered_peaks.bed -fo ES_D10_H3K27ac_filtered_peaks.fasta -name
-
+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
-
-# 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
-meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D0_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D0_H3K27ac_1kb_zoops
-meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D2_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D2_H3K27ac_1kb_zoops
-meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D5_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D5_H3K27ac_1kb_zoops
-meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D7_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D7_H3K27ac_1kb_zoops
-meme -p 64 -dna -mod zoops -nmotifs 15 -minw 8 -maxw 15 -maxsize 20000000 -revcomp ES_D10_H3K27ac_filtered_peaks.fasta -o MEME_op_ES_D10_H3K27ac_1kb_zoops
+# Acutal Processing
+python histone_enhancer_plots.py
--
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