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test_learn.sh
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test_learn.sh
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#!/bin/bash
BAM=/storage/pandaman/project/asimon-data/ENCFF431YXJ.marked.bam
PEAKS=/storage/pandaman/project/asimon-data/ENCFF878DLA.bed
#BAM=/storage/mlamkin/projects/asimon-chip-sim/power-analysis/data/MCF-7/H3K27ac/ENCFF548YRU.flagged.bam
#PEAKS=/storage/mlamkin/projects/asimon-chip-sim/power-analysis/data/MCF-7/H3K27ac/ENCFF187RUK.bed
#BAM=/storage/mlamkin/projects/asimon-chip-sim/power-analysis/data/MCF-7/H3K9me3/ENCFF689XXY.flagged.bam
#PEAKS=/storage/mlamkin/projects/asimon-chip-sim/power-analysis/data/MCF-7/H3K9me3/ENCFF443NFW.bed
#BAM=/storage/mlamkin/projects/asimon-chip-sim/power-analysis/data/MCF-7/FOXA1/ENCFF287PVI.flagged.bam
#PEAKS=/storage/mlamkin/projects/asimon-chip-sim/power-analysis/data/MCF-7/FOXA1/ENCFF017WRM.bed
TYPE=bed
OUTDIR=/home/pandaman/projects/asimon/asimon-chip-sim/test/
THRES=250
COLUMN=7
./src/chipmunk learn \
-p ${PEAKS} \
-b ${BAM} \
-t ${TYPE} \
-o ${OUTDIR}\
-c ${COLUMN}\
--thres ${THRES}\
--paired