/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/makewiggle-stranded-2x36mers.sh:python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- L5674-HEK_Input_post_spin.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5674-HEK_Input_post_spin.2x36mers.unique.dedup.plus.wig -notitle -RPM -uniqueBAM -stranded +
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/makewiggle-stranded-2x36mers.sh:python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- L5674-HEK_Input_post_spin.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5674-HEK_Input_post_spin.2x36mers.unique.dedup.minus.wig -notitle -RPM -uniqueBAM -stranded -
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/map-1x36mers.sh:python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py L5674-HEK_Input_post_spin.260324_NB551514_0424_AHCH32BGY2.end1.fastq.gz 36 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L5674-HEK_Input_post_spin.1x36mers.unique
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/map-2x36mers.sh:python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py L5674-HEK_Input_post_spin.260324_NB551514_0424_AHCH32BGY2.end1.fastq.gz L5674-HEK_Input_post_spin.260324_NB551514_0424_AHCH32BGY2.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38-male.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - L5674-HEK_Input_post_spin.2x36mers.unique
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/MarkDuplicates.sh:module load java; java -Xmx4G -jar /oak/stanford/groups/akundaje/marinovg/programs/picard-tools-1.99/MarkDuplicates.jar INPUT=L5674-HEK_Input_post_spin.2x36mers.unique.bam OUTPUT=L5674-HEK_Input_post_spin.2x36mers.unique.dedup.bam METRICS_FILE=L5674-HEK_Input_post_spin.2x36mers.unique.dedup.metric VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/PEInsertDistFromBAM-2x36mers.sh:python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py L5674-HEK_Input_post_spin.2x36mers.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5674-HEK_Input_post_spin.2x36mers.unique.dedup.InsertLength -uniqueBAM -normalize
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/run_spp.sh:Rscript ~/code/spp/spp_package/run_spp.R -c=L5674-HEK_Input_post_spin.1x36mers.unique.bam -p=20 -savp -rf -s=-0:2:400 -out=L5674-HEK_Input_post_spin.1x36mers.QC
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/samtools-index-1x36mers.sh:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools index L5674-HEK_Input_post_spin.1x36mers.unique.bam
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/samtools-index-2x36mers.sh:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools index L5674-HEK_Input_post_spin.2x36mers.unique.bam
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/samtools-index-2x36mers.sh:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools index L5674-HEK_Input_post_spin.2x36mers.unique.dedup.bam
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/wigtobigwig-wigplusminus-2x36mers.sh:/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig L5674-HEK_Input_post_spin.2x36mers.unique.dedup.plus.wig /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5674-HEK_Input_post_spin.2x36mers.unique.dedup.plus.bigWig
/oak/stanford/groups/akundaje/marinovg/ENCODE4/ChIP/2026-03-24-NextSeq-run/wigtobigwig-wigplusminus-2x36mers.sh:/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig L5674-HEK_Input_post_spin.2x36mers.unique.dedup.minus.wig /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes L5674-HEK_Input_post_spin.2x36mers.unique.dedup.minus.bigWig