Commit d1d6da66 authored by Neva C. Durand's avatar Neva C. Durand
Browse files

proper name for file for qc_apa

parent 6cb20e29

SLURM/scripts/GSE63525_GM12878_primary_replicate_HiCCUPS_looplist_with_motifs_unique_localized.txt

0 → 100644
+2858 −0

File added.

Preview size limit exceeded, changes collapsed.

SLURM/scripts/juicer.sh

+1 −2
Changes for SLURM/scripts/juicer.sh: 1 added line, 2 removed lines.
Original line number Diff line number Diff line
@@ -191,7 +191,6 @@ justHelp="* -j: just exact duplicates excluded at dedupping step" 
earlyexitHelp="* -e: Use for an early exit, before the final creation of the hic files"

helpHelp="* -h: print this help and exit"





printHelpAndExit() {

    echo -e "$usageHelp"

    echo -e "$genomeHelp"
@@ -1409,7 +1408,7 @@ then 
	date

	export IBM_JAVA_OPTIONS="-Xmx4000m -Xgcthreads1"                                                                    

        export _JAVA_OPTIONS="-Xmx4000m -Xms4000m" 

	java -jar ${juiceDir}/scripts/juicer_3.25.21_aggNormAPA.jar apa --ag-norm -k NONE -n 300 -w 100 -r 1000 -q 60 --threads 1 $outputdir/inter_30.hic ${juiceDir}/scripts/GSE63525_GM12878_primary+replicate_HiCCUPS_looplist_with_motifs_unique_localized.txt $outputdir/qc_apa

	java -jar ${juiceDir}/scripts/juicer_3.25.21_aggNormAPA.jar apa --ag-norm -k NONE -n 300 -w 100 -r 1000 -q 60 --threads 1 $outputdir/inter_30.hic ${juiceDir}/scripts/GSE63525_GM12878_primary_replicate_HiCCUPS_looplist_with_motifs_unique_localized.txt $outputdir/qc_apa

	date

QC`

fi

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