Unverified Commit f5879479 authored by Jihed Chouaref's avatar Jihed Chouaref Committed by GitHub
Browse files

Merge pull request #2 from JihedC/main

Main
parents 2d67f3da ff65f167
......@@ -90,22 +90,9 @@ wildcard_constraints:
##############
FASTP = expand(WORKING_DIR + "trimmed/" + "{sample}_{read}_trimmed.fq.gz", sample=SAMPLES, read={"R1", "R2"})
BOWTIE2 = expand(WORKING_DIR + "mapped/{sample}.bam", sample= SAMPLES)
FASTQC = expand(RESULT_DIR + "fastqc/{sample}.fastqc.html", sample = SAMPLES)
FASTQC_REPORTS = expand(RESULT_DIR + "fastqc/{sample}.fastqc.zip", sample=SAMPLES)
BAM_INDEX = expand(RESULT_DIR + "mapped/{sample}.sorted.rmdup.bam.bai", sample=SAMPLES)
BIGWIG = expand(RESULT_DIR + "bigwig/{sample}.bw", sample=SAMPLES)
BED_NARROW = expand(RESULT_DIR + "bed/{sample}_peaks.narrowPeak", sample=SAMPLES)
MULTIBAMSUMMARY = RESULT_DIR + "multiBamSummary/MATRIX.npz"
PLOTCORRELATION = RESULT_DIR + "plotCorrelation/MATRIX.png"
COMPUTEMATRIX = expand(RESULT_DIR + "computematrix/{sample}.{type}.gz", sample=SAMPLES, type={"TSS", "scale-regions"})
HEATMAP = expand(RESULT_DIR + "heatmap/{sample}.{type}.pdf", sample=SAMPLES, type={"TSS", "scale-regions"})
PLOTFINGERPRINT = RESULT_DIR + "plotFingerprint/Fingerplot.pdf"
PLOTPROFILE_PDF = expand(RESULT_DIR + "plotProfile/{sample}.{type}.pdf", sample=SAMPLES, type={"TSS", "scale-regions"})
PLOTPROFILE_BED = expand(RESULT_DIR + "plotProfile/{sample}.{type}.bed", sample=SAMPLES, type={"TSS", "scale-regions"})
MULTIQC = "qc/multiqc.html"
FRAGMENTSIZE = RESULT_DIR + "bamPEFragmentSize/fragmentSize.png"
PLOTCOVERAGE = RESULT_DIR + "plotCoverage/Coverage.png"
FASTQC = expand(RESULT_DIR + "fastqc/{sample}.fastqc.html", sample=SAMPLES)
BIGWIG = expand(RESULT_DIR + "bigwig/{sample}_rpkm.bw", sample=SAMPLES)
MACS2 = expand(RESULT_DIR + "macs2/{treatment}_vs_{control}_peaks.narrowPeak", treatment = CASES, control = CONTROLS)
###############
# Final output
......@@ -114,10 +101,17 @@ rule all:
input:
FASTP,
FASTQC,
BOWTIE2
BOWTIE2,
BIGWIG,
MACS2
message: "ChIP-seq SE pipeline succesfully run." #finger crossed to see this message!
shell:"#rm -rf {WORKING_DIR}"
shell:"""
cp units.tsv RESULT_DIR
cp config.yaml RESULT_DIR
#rm -rf {WORKING_DIR}
"""
###############
# Rules
......@@ -125,19 +119,6 @@ rule all:
include : "rules/external_data.smk"
include : 'rules/pre_processing.smk'
include : "rules/macs2_peak_calling.smk"
include : "rules/peak_calling.smk"
include : "rules/deeptools_post_processing.smk"
rule multiqc:
input:
expand(RESULT_DIR + "fastqc/{sample}.fastqc.zip", sample= SAMPLES),
expand(RESULT_DIR + "bed/{treatment}_vs_{control}_peaks.xls", zip, treatment = CASES, control = CONTROLS)
output:
"qc/multiqc.html"
params:
"" # Optional: extra parameters for multiqc.
log:
"logs/multiqc.log"
wrapper:
"0.27.1/bio/multiqc"
---
samples: sample.tsv
units: units.tsv
units: units_histone.tsv
# files and directories
#fastq_dir: "fastq/"
......@@ -38,69 +38,18 @@ bowtie2:
sensitivity: "--very-sensitive-local"
verbose: "-q"
#Parameters for bamCoverage:
#BAMCOVERAGE
# bamCoverage --bam {input} -o {output} --effectiveGenomeSize
# --effectiveGenomeSize The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. Also, if repetitive regions were not included in the mapping of
# reads, the effective genome size needs to be adjusted accordingly.
bamcoverage:
binsize: '10'
normalizeUsing: 'RPKM'
effectiveGenomeSize: '2652783500' #https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
smoothLength: '50'
bamCoverage:
params:
EFFECTIVEGENOMESIZE: '820000000' #source = http://plant-plasticity.github.io/resources/3_ATAC-seq%20data%20processing.pdf #option is --effectiveGenomeSize
EXTENDREADS: '200' # extend each reads with a 200bp to match the average fragment size of the ChIP experiment
binSize: "1000"
ignoreForNormalization: "SL3.0ch00" #list here space-delimited chromosomes that should be ignored for normalization, sex chromosomes usually.
smoothLength: "40"
normalizeUsing: "RPKM"
bamcompare:
binSize: "1000"
normalizeUsing: "RPKM" #others choices are CPM, BPM, RPGC, None more documentation:https://deeptools.readthedocs.io/en/develop/content/tools/bamCompare.html?highlight=bamcompare
EFFECTIVEGENOMESIZE: '820000000'
operation : "log2" #others choices are ratio, subtract, add, mean, reciprocal_ratio, first, second more documentation:https://deeptools.readthedocs.io/en/develop/content/tools/bamCompare.html?highlight=bamcompare
smoothLength: "40"
scaleFactorsMethod: "None" #others choices are readCount, ,SES
ignoreForNormalization: "SL3.0ch00" #list here space-delimited chromosomes that should be ignored for normalization, sex chromosomes usually.
# macs2 Parameters:
# for information over macs2, refer to https://github.com/taoliu/MACS
# regular peak calling : macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01
# broad peak calling : macs2 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1
#MACS2
macs2:
genomesize: "--gsize mm" #here I used 'mm' because it's the closest to tomato, for human change to 'hs'
format: "--format BAM" #Use BAMPE to activate the paired end data, MACS will use the actual insert size of pairs of reads to build the fragemnt pileup.
format: "--format BAMPE" #Use BAMPE to activate the paired end data, MACS will use the actual insert size of pairs of reads to build the fragemnt pileup.
qvalue: "0.05" #default is 0.05
outdir : "results/bed/"
bandwidth: "--bw 350" #the bandwidth is used to scan the genome for model building. To be set to the expected sonication fragment size.
multiBamSummary:
binSize: "10"
extendReads: "500" #this parameter is necessary when dealing with SE data
computeMatrix:
binSize : "10"
upstream : "3000"
downstream: "3000"
plotCorrelation:
corMethod : "pearson" # Can be replaced by spearman
whatToPlot: "heatmap" # Can be replaced by scatterplot
color : "PuBuGn" # see [here](https://matplotlib.org/examples/color/colormaps_reference.html) for alternative colors
plotHeatmap:
kmeans : "1"
color : "PuBuGn"
plot : "plot, heatmap and colorbar" # Others options are : “plot and heatmap”, “heatmap only” and “heatmap and colorbar”
plotFingerprint:
EXTENDREADS: '200'
binSize: "10"
plotProfile:
kmeans : "1" # choose the number of kmeans to compute
startLabel : "TSS" # default is TSS but could be anything, like "peak start"
endLabel : "TES" # TES is default but can be changed like for startLabel
rule bamCoverage:
rule bamcoverage:
input:
RESULT_DIR + "mapped/{sample}.sorted.rmdup.bam"
bam = RESULT_DIR + "mapped/{sample}.sorted.bam",
bai = RESULT_DIR + "mapped/{sample}.sorted.bam.bai"
output:
RESULT_DIR + "bigwig/{sample}.bw"
bigwig = RESULT_DIR + "bigwig/{sample}_rpkm.bw"
message:
"Converting {wildcards.sample} bam into bigwig file"
"Create genome coverage tracks"
benchmark:
RESULT_DIR + "benchmark/bamcoverage_{sample}.benchmark.txt"
params:
binsize = config["bamcoverage"]["binsize"],
normalizeUsing = config["bamcoverage"]["normalizeUsing"],
effectiveGenomeSize = config["bamcoverage"]["effectiveGenomeSize"],
smoothLength = config["bamcoverage"]["smoothLength"]
log:
RESULT_DIR + "logs/deeptools/{sample}_bamtobigwig.log"
params:
EFFECTIVEGENOMESIZE = str(config["bamCoverage"]["params"]["EFFECTIVEGENOMESIZE"]), #take argument separated as a list separated with a space
EXTENDREADS = str(config["bamCoverage"]["params"]["EXTENDREADS"]),
binSize = str(config['bamCoverage']["params"]['binSize']),
normalizeUsing = str(config['bamCoverage']["params"]['normalizeUsing']),
ignoreForNormalization = str(config['bamCoverage']["params"]['ignoreForNormalization']),
smoothLength = str(config['bamCoverage']["params"]['smoothLength'])
conda:
"../envs/deeptools.yaml"
shell:
"bamCoverage --bam {input} \
-o {output} \
--effectiveGenomeSize {params.EFFECTIVEGENOMESIZE} \
--extendReads {params.EXTENDREADS} \
--binSize {params.binSize} \
--smoothLength {params.smoothLength} \
--ignoreForNormalization {params.ignoreForNormalization} \
&>{log}"
# rule bamcompare:
# input:
# treatment = RESULT_DIR + "mapped/{treatment}.sorted.rmdup.bam", #input requires an indexed bam file
# control = RESULT_DIR + "mapped/{control}.sorted.rmdup.bam" #input requires an indexed bam file
# output:
# bigwig = RESULT_DIR + "bamcompare/log2_{treatment}_{control}.bamcompare.bw"
# message:
# "Running bamCompare for {wildcards.treatment} and {wildcards.control}"
# log:
# RESULT_DIR + "logs/deeptools/log2_{treatment}_{control}.bamcompare.bw.log"
# conda:
# "../envs/deeptools.yaml"
# params:
# binSize = str(config['bamcompare']['binSize']),
# normalizeUsing = str(config['bamcompare']['normalizeUsing']),
# EFFECTIVEGENOMESIZE = str(config["bamcompare"]["EFFECTIVEGENOMESIZE"]),
# operation = str(config['bamcompare']['operation']),
# smoothLength = str(config['bamcompare']['smoothLength']),
# ignoreForNormalization = str(config['bamcompare']['ignoreForNormalization']),
# scaleFactorsMethod = str(config['bamcompare']['scaleFactorsMethod'])
# shell:
# "bamCompare -b1 {input.treatment} \
# -b2 {input.control} \
# --binSize {params.binSize} \
# -o {output.bigwig} \
# --normalizeUsing {params.normalizeUsing} \
# --operation {params.operation} \
# --smoothLength {params.smoothLength} \
# --ignoreForNormalization {params.ignoreForNormalization} \
# --scaleFactorsMethod {params.scaleFactorsMethod} \
# &>{log}"
rule multiBamSummary:
input:
lambda wildcards: expand(RESULT_DIR + "mapped/{sample}.sorted.rmdup.bam", sample = SAMPLES)
output:
RESULT_DIR + "multiBamSummary/MATRIX.npz"
message:
"Computing the read coverage into a numpy array "
threads: 10
params:
binSize = str(config['multiBamSummary']['binSize']),
extendReads = str(config['multiBamSummary']['extendReads'])
log:
RESULT_DIR + "logs/deeptools/multibamsummary/MATRIX.log"
shell:
"multiBamSummary bins \
--bamfiles {input} \
--numberOfProcessors {threads}\
--binSize {params.binSize} \
--centerReads \
--extendReads {params.extendReads} \
-o {output} \
2> {log}"
rule plotCorrelation:
input:
RESULT_DIR + "multiBamSummary/MATRIX.npz"
output:
RESULT_DIR + "plotCorrelation/MATRIX.png"
log:
RESULT_DIR + "logs/deeptools/plotcorrelation/MATRIX.log"
params:
corMethod = str(config['plotCorrelation']['corMethod']),
whatToPlot = str(config['plotCorrelation']['whatToPlot']),
color = str(config['plotCorrelation']['color'])
conda:
"../envs/deeptools.yaml"
message:
"Preparing the correlation plot between all samples"
shell:
"plotCorrelation \
--corData {input} \
--corMethod {params.corMethod} \
--whatToPlot {params.whatToPlot} \
--skipZeros \
--colorMap {params.color} \
--plotFile {output} \
--plotNumbers \
2> {log}"
#--plotTitle 'Pearson Correlation of {params.title} coverage' \
rule computeMatrix:
input:
bigwig = RESULT_DIR + "bigwig/{sample}.bw",
bed = WORKING_DIR + "gene_model.gtf"
output:
RESULT_DIR + "computematrix/{sample}.TSS.gz"
threads: 10
params:
binSize = str(config['computeMatrix']['binSize']),
upstream = str(config['computeMatrix']['upstream']),
downstream = str(config['computeMatrix']['downstream'])
conda:
"../envs/deeptools.yaml"
log:
RESULT_DIR + "logs/deeptools/computematrix/{sample}.log"
message:
"Computing matrix for {input.bigwig} with {params.binSize} bp windows and {params.upstream} bp around TSS"
shell:
"computeMatrix \
reference-point \
--referencePoint TSS \
-S {input.bigwig} \
-R {input.bed} \
--afterRegionStartLength {params.upstream} \
--beforeRegionStartLength {params.downstream} \
--numberOfProcessors {threads} \
--binSize {params.binSize} \
-o {output} \
2> {log}"
rule computeMatrix_scale:
input:
bigwig = RESULT_DIR + "bigwig/{sample}.bw",
bed = WORKING_DIR + "gene_model.gtf"
output:
RESULT_DIR + "computematrix/{sample}.scale-regions.gz"
threads: 10
params:
binSize = str(config['computeMatrix']['binSize']),
upstream = str(config['computeMatrix']['upstream']),
downstream = str(config['computeMatrix']['downstream'])
conda:
"../envs/deeptools.yaml"
log:
RESULT_DIR + "logs/deeptools/computematrix/{sample}.log"
shell:
"computeMatrix \
scale-regions \
-S {input.bigwig} \
-R {input.bed} \
--afterRegionStartLength {params.upstream} \
--beforeRegionStartLength {params.downstream} \
--numberOfProcessors {threads} \
--binSize {params.binSize} \
-o {output} \
2> {log}"
rule plotHeatmap:
input:
RESULT_DIR + "computematrix/{sample}.{type}.gz"
output:
RESULT_DIR + "heatmap/{sample}.{type}.pdf"
params:
kmeans = str(config['plotHeatmap']['kmeans']),
color = str(config['plotHeatmap']['color']),
plot = str(config['plotHeatmap']['plot']),
cluster = RESULT_DIR + "heatmap/{sample}.bed"
conda:
"../envs/deeptools.yaml"
log:
RESULT_DIR + "logs/deeptools/plotHeatmap/{sample}.{type}.log"
message:
"Preparing Heatmaps..."
shell:
"plotHeatmap \
--matrixFile {input} \
--outFileName {output} \
--kmeans {params.kmeans} \
--colorMap {params.color} \
--legendLocation best \
--outFileSortedRegions {params.cluster}"
rule plotFingerprint:
input:
expand(RESULT_DIR + "mapped/{sample}.sorted.rmdup.bam", sample = SAMPLES)
output:
pdf = RESULT_DIR + "plotFingerprint/Fingerplot.pdf"
params:
EXTENDREADS = str(config["bamCoverage"]["params"]["EXTENDREADS"]),
binSize = str(config['bamCoverage']["params"]['binSize'])
conda:
"../envs/deeptools.yaml"
message:
"Preparing deeptools plotFingerprint"
shell:
"plotFingerprint \
-b {input} \
--extendReads {params.EXTENDREADS} \
--binSize {params.binSize} \
--plotFile {output}"
rule plotProfile:
input:
RESULT_DIR + "computematrix/{sample}.{type}.gz"
output:
pdf = RESULT_DIR + "plotProfile/{sample}.{type}.pdf",
bed = RESULT_DIR + "plotProfile/{sample}.{type}.bed"
params:
kmeans = str(config['plotProfile']['kmeans']),
startLabel = str(config['plotProfile']['startLabel']),
endLabel = str(config['plotProfile']['endLabel'])
conda:
"../envs/deeptools.yaml"
log:
RESULT_DIR + "logs/deeptools/plotProfile/{sample}.{type}.log"
message:
"Preparing deeptools plotProfile"
RESULT_DIR + "log/bamcoverage/{sample}.log"
shell:
"plotProfile \
--matrixFile {input} \
--outFileName {output.pdf} \
--outFileSortedRegions {output.bed} \
--kmeans {params.kmeans} \
--startLabel {params.startLabel} \
--endLabel {params.endLabel}"
"bamCoverage -b {input.bam} --binSize {params.binsize} --effectiveGenomeSize {params.effectiveGenomeSize} --normalizeUsing {params.normalizeUsing} --smoothLength {params.smoothLength} -o {output.bigwig} 2>{log}"
rule call_narrow_peaks:
input:
treatment = RESULT_DIR + "mapped/{treatment}.sorted.bam",
control = RESULT_DIR + "mapped/{control}.sorted.bam",
output:
RESULT_DIR + "macs2/{treatment}_vs_{control}_peaks.narrowPeak"
message:
"Calling narrowPeak for {wildcards.sample}"
params:
name = "{treatment}_vs_{control}", #this option will give the output name, has to be similar to the output
genomesize = str(config['macs2']['genomesize']),
qvalue = str(config['macs2']['qvalue'])
log:
RESULT_DIR + "logs/macs2/{treatment}_vs_{control}_peaks.narrowPeak.log"
shell:
"macs2 callpeak -t {input.treatment} -c {input.control} {params.genomesize} --name {params.name} -q {params.qvalue} --nomodel --outdir results/bed/ &>{log}"
################## Rules used for QC ##################
rule fastp:
input:
get_fastq
......@@ -73,38 +71,31 @@ rule align:
shell("bowtie2 --very-sensitive --threads {threads} -x {params.index} \
-U {input.forward_read} | samtools view -Sb - > {output.bams} 2>{log}")
else:
shell("bowtie2 --very-sentitive --threads {threads} -x {params.index} \
-1 {input.forward_read} -2 {input.reverse_read} samtools view -Sb - > {output.bams} 2>{log}")
shell("bowtie2 --very-sensitive --threads {threads} -x {params.index} \
-1 {input.forward_read} -2 {input.reverse_read} | samtools view -Sb - > {output.bams} 2>{log}")
rule sort:
input:
WORKING_DIR + "mapped/{sample}.bam"
output:
temp(RESULT_DIR + "mapped/{sample}.sorted.bam")
bam = RESULT_DIR + "mapped/{sample}.sorted.bam"
message:"Sorting {wildcards.sample} bam file"
threads: 10
log:
RESULT_DIR + "logs/samtools/{sample}.sort.log"
conda:
"../envs/samtools.yaml"
shell:
"samtools sort -@ {threads} -o {output} {input} &>{log}"
"""
samtools sort -@ {threads} -o {output.bam} {input} &>{log}
samtools index {output.bam}
"""
rule rmdup:
rule index_bam:
input:
RESULT_DIR + "mapped/{sample}.sorted.bam"
output:
bam = RESULT_DIR + "mapped/{sample}.sorted.rmdup.bam",
bai = RESULT_DIR + "mapped/{sample}.sorted.rmdup.bam.bai" #bai files required for the bigwig and bamCompare rules
message: "Removing duplicate from file {wildcards.sample}"
RESULT_DIR + "mapped/{sample}.sorted.bam.bai"
log:
RESULT_DIR + "logs/samtools/{sample}.sorted.rmdup.bam.log"
conda:
"../envs/samtools.yaml"
RESULT_DIR + "log/sort/{sample}.log"
shell:
"""
samtools rmdup -s {input} {output.bam} &>{log}
samtools index {output.bam}
"""
#samtools manual says "This command is obsolete. Use markdup instead
"samtools index {input} 2>{log}"
......@@ -6,7 +6,9 @@
#SBATCH -t 24:00:00
#SBATCH --mem=15000
module purge
module load genomics/ngs/samtools/1.11/gcc-8.3.1
module load genomics/ngs/aligners/bowtie2/2.4.2/gcc-8.3.1
echo Start time : `date`
snakemake -p \
--snakefile Snakefile \
......
sample fq1 fq2 condition
H3K9AcDN1rep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091645_T1.fastq.gz treatment
H3K9AcDN1rep2 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091645_T2.fastq.gz treatment
H3K9AcDN1rep3 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091646_T1.fastq.gz treatment
H3K9AcDN2arep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091647_T1.fastq.gz treatment
H3K9AcDN2brep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091648_T1.fastq.gz treatment
H3K9AcDN2brep2 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091648_T2.fastq.gz treatment
H3K9AcDN2brep3 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091649_T1.fastq.gz treatment
H3K9AcDN2brep4 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091649_T2.fastq.gz treatment
H3K9AcDN3rep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091650_T1.fastq.gz treatment
H3K9AcDN3rep2 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091650_T2.fastq.gz treatment
H3K9AcDN3rep3 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091651_T1.fastq.gz treatment
H3K4me2DN1rep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091654_T1.fastq.gz treatment
H3K4me2DN1rep2 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091654_T2.fastq.gz treatment
H3K4me2DN1rep3 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091655_T1.fastq.gz treatment
H3K4me2DN2arep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091656_T1.fastq.gz treatment
H3K4me2DN2brep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091657_T1.fastq.gz treatment
H3K4me2DN2brep2 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091657_T2.fastq.gz treatment
H3K4me2DN2brep3 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091658_T1.fastq.gz treatment
H3K4me2DN2brep4 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091658_T2.fastq.gz treatment
H3K4me2DN3rep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091659_T1.fastq.gz treatment
H3K4me2DN3rep2 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091659_T2.fastq.gz treatment
H3K4me2DN3rep3 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091660_T1.fastq.gz treatment
H3K27me3DN1rep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091663_T1.fastq.gz treatment
H3K27me3DN1rep2 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091663_T2.fastq.gz treatment
H3K27me3DN1rep3 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091663_T3.fastq.gz treatment
H3K27me3DN1rep4 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091664_T1.fastq.gz treatment
H3K27me3DN1rep5 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091664_T2.fastq.gz treatment
H3K27me3DN2arep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091665_T1.fastq.gz treatment
H3K27me3DN2brep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091666_T1.fastq.gz treatment
H3K27me3DN2brep2 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091666_T2.fastq.gz treatment
H3K27me3DN2brep3 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091667_T1.fastq.gz treatment
H3K27me3DN2brep4 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091667_T2.fastq.gz treatment
H3K27me3DN2brep5 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091668_T1.fastq.gz treatment
H3K27me3DN2brep6 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091668_T2.fastq.gz treatment
H3K27me3DN3rep1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091668_T1.fastq.gz treatment
H3K27me3DN3rep2 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091668_T2.fastq.gz treatment
H3K27me3DN3rep3 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091668_T3.fastq.gz treatment
H3K27me3DN3rep4 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091669_T1.fastq.gz treatment
H3K27me3DN3rep5 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091669_T2.fastq.gz treatment
PU1DN1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091672_T1.fastq.gz treatment
PU1DN2a /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091673_T1.fastq.gz treatment
PU1DN2b /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091674_T1.fastq.gz treatment
GATADN1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091676_T1.fastq.gz treatment
GATADN2b /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091677_T1.fastq.gz treatment
inputDN1 /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091679_T1.fastq.gz control
inputDN2a /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091680_T1.fastq.gz control
inputDN2b /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091681_T1.fastq.gz control
inputDN3a /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091682_T1.fastq.gz control
inputDN3b /exports/humgen/jihed/Kernfeld_scRNA_thymus/nextflow/results/fastq/SRX091682_T2.fastq.gz control
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