From bee1900b0ee6775104160115da69e1b1562d4230 Mon Sep 17 00:00:00 2001
From: jnasser <jnasser@broadinstitute.org>
Date: Thu, 14 Nov 2019 11:12:38 -0500
Subject: [PATCH] fixed untracked files

---
 run.example.sh | 71 --------------------------------------------------
 1 file changed, 71 deletions(-)
 delete mode 100755 run.example.sh

diff --git a/run.example.sh b/run.example.sh
deleted file mode 100755
index 81ef0e69..00000000
--- a/run.example.sh
+++ /dev/null
@@ -1,71 +0,0 @@
-# Test run ABC code
-cd /seq/lincRNA/RAP/Promoters/ABC-Enhancer-Gene-Prediction;
-
-## HiC Section
-# python src/juicebox_dump.py \
-# --hic_file https://hicfiles.s3.amazonaws.com/hiseq/k562/in-situ/combined_30.hic \
-# --juicebox "java -jar /seq/lincRNA/Software/juicer/GridEngine8/scripts/juicer_tools.jar" \
-# --outdir example_chr22/input_data/HiC/raw/ \
-# --chromosomes 22
-
-# python src/compute_powerlaw_fit_from_hic.py \
-# --hicDir example_chr22/input_data/HiC/raw/ \
-# --outDir example_chr22/input_data/HiC/raw/powerlaw/ \
-# --maxWindow 1000000 \
-# --minWindow 5000 \
-# --resolution 5000 \
-# --chr 'chr22'
-
-#Peaks
-use MACS2;
-macs2 callpeak \
--t example_chr22/input_data/Chromatin/wgEncodeUwDnaseK562AlnRep1.chr22.bam \
--n wgEncodeUwDnaseK562AlnRep1.chr22.macs2 \
--f BAM \
--g hs \
--p .1 \
---call-summits \
---outdir example_chr22/ABC_output/Peaks/ 
-
-unuse MACS2;
-source /seq/lincRNA/thouis/VENV36/bin/activate;
-use .samtools-1.8;
-
-#Sort narrowPeak file
-bedtools sort -faidx example_chr22/reference/chr22 -i example_chr22/ABC_output/Peaks/wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak > example_chr22/ABC_output/Peaks/wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.sorted
-
-python src/makeCandidateRegions.py \
---narrowPeak example_chr22/ABC_output/Peaks/wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.sorted \
---bam example_chr22/input_data/Chromatin/wgEncodeUwDnaseK562AlnRep1.chr22.bam \
---outDir example_chr22/ABC_output/Peaks/ \
---chrom_sizes example_chr22/reference/chr22 \
---regions_blacklist reference/wgEncodeHg19ConsensusSignalArtifactRegions.bed \
---regions_whitelist example_chr22/reference/RefSeqCurated.170308.bed.CollapsedGeneBounds.TSS.500bp.chr22.bed \
---peakExtendFromSummit 250 \
---nStrongestPeaks 3000 
-
-#Nbhds
-python src/run.neighborhoods.py \
---candidate_enhancer_regions example_chr22/ABC_output/Peaks/wgEncodeUwDnaseK562AlnRep1.chr22.macs2_peaks.narrowPeak.sorted.candidateRegions.bed \
---genes example_chr22/reference/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.bed \
---H3K27ac example_chr22/input_data/Chromatin/ENCFF384ZZM.chr22.bam \
---DHS example_chr22/input_data/Chromatin/wgEncodeUwDnaseK562AlnRep1.chr22.bam,example_chr22/input_data/Chromatin/wgEncodeUwDnaseK562AlnRep2.chr22.bam \
---expression_table example_chr22/input_data/Expression/K562.ENCFF934YBO.TPM.txt \
---chrom_sizes example_chr22/reference/chr22 \
---ubiquitously_expressed_genes reference/UbiquitouslyExpressedGenesHG19.txt \
---cellType K562 \
---outdir example_chr22/ABC_output/Neighborhoods/ 
-
-#Preds
-python src/predict.py \
---enhancers example_chr22/ABC_output/Neighborhoods/EnhancerList.txt \
---genes example_chr22/ABC_output/Neighborhoods/GeneList.txt \
---HiCdir example_chr22/input_data/HiC/raw/ \
---hic_resolution 5000 \
---scale_hic_using_powerlaw \
---threshold .02 \
---cellType K562 \
---outdir example_chr22/ABC_output/Predictions/ \
---make_all_putative
-
-