GSE124714 Processing Pipeline
Publication
The mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics.Current biology : CB (2020) — PMID 31983639
Dataset
GSE124714The mRNA decay factor CAR-1 regulates axon regeneration via mitochondrial calcium dynamics
Processing Steps
Generate Jupyter Notebook-
1
(Using CZ25180_S1_L008_R1_001.fastq.gz as an example starting fastq file): umi_tools extract --stdin CZ25180_S1_L008_R1_001.fastq.gz --bc-pattern NNNNNNNNNN --log CAR1.CZ25180_IP.---.--.metrics CAR1 --stdout CAR1.CZ25180_IP.umi.r1.fq
$ Bash example
# Install UMI-tools (example using conda) # conda install -c bioconda umi-tools=1.1.2 umi_tools extract --stdin CZ25180_S1_L008_R1_001.fastq.gz --bc-pattern NNNNNNNNNN --log CAR1.CZ25180_IP.---.--.metrics CAR1 --stdout CAR1.CZ25180_IP.umi.r1.fq
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2
cutadapt -O \ 1 \ -f \ fastq \ --match-read-wildcards \ --times \ 1 \ -e \ 0.1 \ --quality-cutoff \ 6 \ -m \ 18 \ -o \ CAR1.CZ25180_IP.umi.r1Tr.fq \ '-a AGATCGGAAGAGCAC' \ '-a GATCGGAAGAGCACA' \ '-a ATCGGAAGAGCACAC' \ '-a TCGGAAGAGCACACG' \ '-a CGGAAGAGCACACGT' \ '-a GGAAGAGCACACGTC' \ '-a GAAGAGCACACGTCT' \ '-a AAGAGCACACGTCTG' \ '-a AGAGCACACGTCTGA' \ '-a GAGCACACGTCTGAA' \ '-a AGCACACGTCTGAAC' \ '-a GCACACGTCTGAACT' \ '-a CACACGTCTGAACTC' \ '-a ACACGTCTGAACTCC' \ '-a CACGTCTGAACTCCA' \ '-a ACGTCTGAACTCCAG' \ '-a CGTCTGAACTCCAGT' \ '-a GTCTGAACTCCAGTC' \ '-a TCTGAACTCCAGTCA' \ '-a CTGAACTCCAGTCAC' \ CAR1.CZ25180_IP.umi.r1.fq
$ Bash example
# Install cutadapt (e.g., using conda) # conda install -c bioconda cutadapt=1.18 cutadapt -O 1 -f fastq --match-read-wildcards --times 1 -e 0.1 --quality-cutoff 6 -m 18 -o CAR1.CZ25180_IP.umi.r1Tr.fq \ '-a AGATCGGAAGAGCAC' \ '-a GATCGGAAGAGCACA' \ '-a ATCGGAAGAGCACAC' \ '-a TCGGAAGAGCACACG' \ '-a CGGAAGAGCACACGT' \ '-a GGAAGAGCACACGTC' \ '-a GAAGAGCACACGTCT' \ '-a AAGAGCACACGTCTG' \ '-a AGAGCACACGTCTGA' \ '-a GAGCACACGTCTGAA' \ '-a AGCACACGTCTGAAC' \ '-a GCACACGTCTGAACT' \ '-a CACACGTCTGAACTC' \ '-a ACACGTCTGAACTCC' \ '-a CACGTCTGAACTCCA' \ '-a ACGTCTGAACTCCAG' \ '-a CGTCTGAACTCCAGT' \ '-a GTCTGAACTCCAGTC' \ '-a TCTGAACTCCAGTCA' \ '-a CTGAACTCCAGTCAC' \ CAR1.CZ25180_IP.umi.r1.fq
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3
cutadapt \ -O \ 5 \ -f \ fastq \ --match-read-wildcards \ --times \ 1 \ -e \ 0.1 \ --quality-cutoff \ 6 \ -m \ 18 \ -o \ CAR1.CZ25180_IP.umi.r1TrTr.fq \ -a AGATCGGAAGAGCAC \ -a GATCGGAAGAGCACA \ -a ATCGGAAGAGCACAC \ -a TCGGAAGAGCACACG \ -a CGGAAGAGCACACGT \ -a GGAAGAGCACACGTC \ -a GAAGAGCACACGTCT \ -a AAGAGCACACGTCTG \ -a AGAGCACACGTCTGA \ -a GAGCACACGTCTGAA \ -a AGCACACGTCTGAAC \ -a GCACACGTCTGAACT \ -a CACACGTCTGAACTC \ -a ACACGTCTGAACTCC \ -a CACGTCTGAACTCCA \ -a ACGTCTGAACTCCAG \ -a CGTCTGAACTCCAGT \ -a GTCTGAACTCCAGTC \ -a TCTGAACTCCAGTCA \ -a CTGAACTCCAGTCAC \ CAR1.CZ25180_IP.umi.r1Tr.fq
$ Bash example
cutadapt \ -O 5 \ -f fastq \ --match-read-wildcards \ --times 1 \ -e 0.1 \ --quality-cutoff 6 \ -m 18 \ -o CAR1.CZ25180_IP.umi.r1TrTr.fq \ -a AGATCGGAAGAGCAC \ -a GATCGGAAGAGCACA \ -a ATCGGAAGAGCACAC \ -a TCGGAAGAGCACACG \ -a CGGAAGAGCACACGT \ -a GGAAGAGCACACGTC \ -a GAAGAGCACACGTCT \ -a AAGAGCACACGTCTG \ -a AGAGCACACGTCTGA \ -a GAGCACACGTCTGAA \ -a AGCACACGTCTGAAC \ -a GCACACGTCTGAACT \ -a CACACGTCTGAACTC \ -a ACACGTCTGAACTCC \ -a CACGTCTGAACTCCA \ -a ACGTCTGAACTCCAG \ -a CGTCTGAACTCCAGT \ -a GTCTGAACTCCAGTC \ -a TCTGAACTCCAGTCA \ -a CTGAACTCCAGTCAC \ CAR1.CZ25180_IP.umi.r1Tr.fq
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4
fastq-sort --id CAR1.CZ25180_IP.umi.r1TrTr.fq > CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq
fastq-sort (Inferred with models/gemini-2.5-flash) v0.2.0 (Inferred with models/gemini-2.5-flash)$ Bash example
# Install fastq-sort (e.g., using conda) # conda install -c bioconda fastq-sort # Execute the fastq-sort command fastq-sort --id CAR1.CZ25180_IP.umi.r1TrTr.fq > CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq
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STAR \ --alignEndsType \ EndToEnd \ --genomeDir \ RepBase18.05.STAR \ --genomeLoad \ NoSharedMemory \ --outBAMcompression \ 10 \ --outFileNamePrefix \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STAR \ --outFilterMultimapNmax \ 30 \ --outFilterMultimapScoreRange \ 1 \ --outFilterScoreMin \ 10 \ --outFilterType \ BySJout \ --outReadsUnmapped \ Fastx \ --outSAMattrRGline \ ID:foo \ --outSAMattributes \ All \ --outSAMmode \ Full \ --outSAMtype \ BAM \ Unsorted \ --outSAMunmapped \ Within \ --outStd \ Log \ --readFilesIn \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq \ --runMode \ alignReads \ --runThreadN \ 8
$ Bash example
# Install STAR (example using conda): # conda install -c bioconda star # Reference dataset: RepBase18.05.STAR is a custom STAR index built from RepBase version 18.05. # Ensure this genome directory is pre-built and accessible. STAR \ --alignEndsType EndToEnd \ --genomeDir RepBase18.05.STAR \ --genomeLoad NoSharedMemory \ --outBAMcompression 10 \ --outFileNamePrefix CAR1.CZ25180_IP.umi.r1TrTr.sorted.STAR \ --outFilterMultimapNmax 30 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --outFilterType BySJout \ --outReadsUnmapped Fastx \ --outSAMattrRGline ID:foo \ --outSAMattributes All \ --outSAMmode Full \ --outSAMtype BAM Unsorted \ --outSAMunmapped Within \ --outStd Log \ --readFilesIn CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq \ --runMode alignReads \ --runThreadN 8
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STAR \ --alignEndsType \ EndToEnd \ --genomeDir \ ce10.STAR \ --genomeLoad \ NoSharedMemory \ --outBAMcompression \ 10 \ --outFileNamePrefix \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STAR \ --outFilterMultimapNmax \ 1 \ --outFilterMultimapScoreRange \ 1 \ --outFilterScoreMin \ 10 \ --outFilterType \ BySJout \ --outReadsUnmapped \ Fastx \ --outSAMattrRGline \ ID:foo \ --outSAMattributes \ All \ --outSAMmode \ Full \ --outSAMtype \ BAM \ Unsorted \ --outSAMunmapped \ Within \ --outStd \ Log \ --readFilesIn \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.fq \ --runMode \ alignReads \ --runThreadN \ 8
$ Bash example
# Install STAR (if not already installed) # conda install -c bioconda star # Align reads using STAR STAR \ --alignEndsType EndToEnd \ --genomeDir ce10.STAR \ --genomeLoad NoSharedMemory \ --outBAMcompression 10 \ --outFileNamePrefix CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STAR \ --outFilterMultimapNmax 1 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --outFilterType BySJout \ --outReadsUnmapped Fastx \ --outSAMattrRGline ID:foo \ --outSAMattributes All \ --outSAMmode Full \ --outSAMtype BAM Unsorted \ --outSAMunmapped Within \ --outStd Log \ --readFilesIn CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.fq \ --runMode alignReads \ --runThreadN 8 # Note: The genome directory 'ce10.STAR' refers to the C. elegans (ce10) genome index. # This index must be pre-built using STAR's genomeGenerate command.
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7
umi_tools \ dedup \ -I \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.bam \ --output-stats \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo \ -S \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDup.bam
$ Bash example
# Install UMI-tools (e.g., using conda) # conda create -n umi_env umi-tools=1.0.1 # conda activate umi_env INPUT_BAM="CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.bam" OUTPUT_PREFIX="CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo" OUTPUT_BAM="${OUTPUT_PREFIX}.rmDup.bam" OUTPUT_STATS="${OUTPUT_PREFIX}" umi_tools dedup \ -I "${INPUT_BAM}" \ --output-stats "${OUTPUT_STATS}" \ -S "${OUTPUT_BAM}" -
8
sort \ -o \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDup.bam
$ Bash example
# Install samtools if not already installed # conda install -c bioconda samtools samtools sort \ -o CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDup.bam
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samtools \ index \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam
$ Bash example
# Install samtools (e.g., via conda) # conda install -c bioconda samtools=1.10 samtools index CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam
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makebigwigfiles \ --bw_pos \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.pos.bw \ --bw_neg \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.neg.bw \ --bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ --genome \ ce10.chrom.sizes
$ Bash example
# Download reference genome sizes file (if not already available) # For C. elegans ce10 # wget https://hgdownload.soe.ucsc.edu/goldenPath/ce10/bigZips/ce10.chrom.sizes -O ce10.chrom.sizes # Assuming 'makebigwigfiles' is an executable script in the current PATH or specified with its full path. # This script is likely a custom wrapper or a modified version of the makebigwigfiles.py script # found in the yeolab/eclip repository, as its parameter interface (--bw_pos, --bw_neg) # differs from the public script's --out_prefix parameter. makebigwigfiles \ --bw_pos CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.pos.bw \ --bw_neg CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.neg.bw \ --bam CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ --genome ce10.chrom.sizes
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clipper \ --bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ --species ce10 \ --outfile CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.bed \ --save-pickle
$ Bash example
# Install CLIPper (if not already installed) # pip install clipper clipper --bam CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam --species ce10 --outfile CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.bed --save-pickle
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samtools view -c -F 4 CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ > CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum
$ Bash example
# Install samtools (e.g., using conda) # conda install -c bioconda samtools=1.10 samtools view -c -F 4 CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam > CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum
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overlap_peakfi_with_bam_PE.pl \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ26430_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.bed \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum \ CAR1.CZ26430_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.bed
$ Bash example
# Install Perl if not available # conda install -c conda-forge perl # Ensure necessary Perl modules are installed (e.g., BioPerl, if used by the script) # conda install -c bioconda bioperl overlap_peakfi_with_bam_PE.pl \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ26430_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.bed \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum \ CAR1.CZ26430_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.bed -
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peakscompress.pl \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.bed \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.compressed.bed
$ Bash example
# Install Perl if not already available # conda install -c conda-forge perl # Clone the clipper repository to get peakscompress.pl # git clone https://github.com/yeolab/clipper.git # export PATH=$PATH:$(pwd)/clipper/bin peakscompress.pl \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.bed \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.compressed.bed
Tools Used
Raw Source Text
(Using CZ25180_S1_L008_R1_001.fastq.gz as an example starting fastq file): umi_tools extract --stdin CZ25180_S1_L008_R1_001.fastq.gz --bc-pattern NNNNNNNNNN --log CAR1.CZ25180_IP.---.--.metrics CAR1 --stdout CAR1.CZ25180_IP.umi.r1.fq cutadapt -O \ 1 \ -f \ fastq \ --match-read-wildcards \ --times \ 1 \ -e \ 0.1 \ --quality-cutoff \ 6 \ -m \ 18 \ -o \ CAR1.CZ25180_IP.umi.r1Tr.fq \ '-a AGATCGGAAGAGCAC' \ '-a GATCGGAAGAGCACA' \ '-a ATCGGAAGAGCACAC' \ '-a TCGGAAGAGCACACG' \ '-a CGGAAGAGCACACGT' \ '-a GGAAGAGCACACGTC' \ '-a GAAGAGCACACGTCT' \ '-a AAGAGCACACGTCTG' \ '-a AGAGCACACGTCTGA' \ '-a GAGCACACGTCTGAA' \ '-a AGCACACGTCTGAAC' \ '-a GCACACGTCTGAACT' \ '-a CACACGTCTGAACTC' \ '-a ACACGTCTGAACTCC' \ '-a CACGTCTGAACTCCA' \ '-a ACGTCTGAACTCCAG' \ '-a CGTCTGAACTCCAGT' \ '-a GTCTGAACTCCAGTC' \ '-a TCTGAACTCCAGTCA' \ '-a CTGAACTCCAGTCAC' \ CAR1.CZ25180_IP.umi.r1.fq cutadapt \ -O \ 5 \ -f \ fastq \ --match-read-wildcards \ --times \ 1 \ -e \ 0.1 \ --quality-cutoff \ 6 \ -m \ 18 \ -o \ CAR1.CZ25180_IP.umi.r1TrTr.fq \ -a AGATCGGAAGAGCAC \ -a GATCGGAAGAGCACA \ -a ATCGGAAGAGCACAC \ -a TCGGAAGAGCACACG \ -a CGGAAGAGCACACGT \ -a GGAAGAGCACACGTC \ -a GAAGAGCACACGTCT \ -a AAGAGCACACGTCTG \ -a AGAGCACACGTCTGA \ -a GAGCACACGTCTGAA \ -a AGCACACGTCTGAAC \ -a GCACACGTCTGAACT \ -a CACACGTCTGAACTC \ -a ACACGTCTGAACTCC \ -a CACGTCTGAACTCCA \ -a ACGTCTGAACTCCAG \ -a CGTCTGAACTCCAGT \ -a GTCTGAACTCCAGTC \ -a TCTGAACTCCAGTCA \ -a CTGAACTCCAGTCAC \ CAR1.CZ25180_IP.umi.r1Tr.fq fastq-sort --id CAR1.CZ25180_IP.umi.r1TrTr.fq > CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq STAR \ --alignEndsType \ EndToEnd \ --genomeDir \ RepBase18.05.STAR \ --genomeLoad \ NoSharedMemory \ --outBAMcompression \ 10 \ --outFileNamePrefix \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STAR \ --outFilterMultimapNmax \ 30 \ --outFilterMultimapScoreRange \ 1 \ --outFilterScoreMin \ 10 \ --outFilterType \ BySJout \ --outReadsUnmapped \ Fastx \ --outSAMattrRGline \ ID:foo \ --outSAMattributes \ All \ --outSAMmode \ Full \ --outSAMtype \ BAM \ Unsorted \ --outSAMunmapped \ Within \ --outStd \ Log \ --readFilesIn \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq \ --runMode \ alignReads \ --runThreadN \ 8 STAR \ --alignEndsType \ EndToEnd \ --genomeDir \ ce10.STAR \ --genomeLoad \ NoSharedMemory \ --outBAMcompression \ 10 \ --outFileNamePrefix \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STAR \ --outFilterMultimapNmax \ 1 \ --outFilterMultimapScoreRange \ 1 \ --outFilterScoreMin \ 10 \ --outFilterType \ BySJout \ --outReadsUnmapped \ Fastx \ --outSAMattrRGline \ ID:foo \ --outSAMattributes \ All \ --outSAMmode \ Full \ --outSAMtype \ BAM \ Unsorted \ --outSAMunmapped \ Within \ --outStd \ Log \ --readFilesIn \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.fq \ --runMode \ alignReads \ --runThreadN \ 8 umi_tools \ dedup \ -I \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.bam \ --output-stats \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo \ -S \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDup.bam sort \ -o \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDup.bam samtools \ index \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam makebigwigfiles \ --bw_pos \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.pos.bw \ --bw_neg \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.neg.bw \ --bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ --genome \ ce10.chrom.sizes clipper \ --bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ --species ce10 \ --outfile CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.bed \ --save-pickle samtools view -c -F 4 CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ > CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum overlap_peakfi_with_bam_PE.pl \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ26430_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.bed \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum \ CAR1.CZ26430_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.bed peakscompress.pl \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.bed \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.compressed.bed Genome_build: ce10 Supplementary_files_format_and_content: bed format, contains peaks of predicted RBP binding