ChIP-seq

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chip-seq
chip-seq
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A Snakemake workflow for ChIP-seq reads alignments with bwa , samtools and deeptools .

Code Snippets

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shell:
	"bamCoverage -b {input.bam} -o {output} -of bigwig -bs {params.binsize} -p {threads} --exactScaling --normalizeUsing {params.normalization} "
SnakeMake DeepTools From line 16 of rules/bamcoverage.smk 
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shell:
	"bwa index -a {params.construction_algorithm} {input} 2> {log}"
SnakeMake BWA From line 11 of rules/bwa.smk 
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shell:
	"bwa mem {params.custom} "
	"-t {threads} "
	"{input.genome} {input.fastq} "
	"> {output} 2> {log}"
SnakeMake BWA From line 31 of rules/bwa.smk 
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shell: 
	"fastqc -q -t {threads} --outdir {params.dir} {input.fastq}"
SnakeMake FastQC From line 16 of rules/fastqc.smk 
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shell:
	"rename 's/_fastqc.zip/_raw_fastqc.zip/' {params.dirraw}/*_fastqc.zip"
SnakeMake From line 27 of rules/fastqc.smk 
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shell: "fastqc -q -t {threads} --outdir {params.dir} {input.bam}"
SnakeMake FastQC From line 44 of rules/fastqc.smk 
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shell:
	"export LC_ALL=C.UTF-8 && "
	"export LANG=C.UTF-8 && "
	"multiqc {params.title} --config {params.conf} --title {params.title} -o {params.output} --filename {params.filename}"
SnakeMake MultiQC From line 62 of rules/fastqc.smk 
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shell:
	"samtools faidx -o {output} {input}"
SnakeMake SAMtools From line 7 of rules/samtools.smk 
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shell:
	"samtools view "
	"{params.custom} -@ {threads} "
	"-b -S "
	"-q {params.quality} "
	"-t {input.genome} "
	"-o {output} "
	"{input.sam}"
SnakeMake SAMtools From line 25 of rules/samtools.smk 
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shell:
	"samtools sort -@ {threads} -n -o {output} "
	"{input.bam} "
SnakeMake SAMtools From line 47 of rules/samtools.smk 
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shell:
	"samtools fixmate -m -@ {threads} "
	"{input.bam} "
	"{output}"
SnakeMake SAMtools From line 62 of rules/samtools.smk 
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shell:
	"samtools sort -@ {threads} "
	"-o {output} "
	"{input.bam}"
SnakeMake SAMtools From line 78 of rules/samtools.smk 
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shell:
	"samtools markdup -@ {threads} -r "
	"{input.bam} "
	"{output}"
SnakeMake SAMtools From line 95 of rules/samtools.smk 
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shell:
	"samtools index -@ {threads} {input} {output}"
SnakeMake SAMtools From line 111 of rules/samtools.smk 
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shell:
	"samtools stats {input.bam} > {output}"
SnakeMake SAMtools From line 126 of rules/samtools.smk 
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shell:
	"samtools idxstats {input.bam} > {output}"
SnakeMake SAMtools From line 140 of rules/samtools.smk 
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shell:
	"samtools flagstat {input.bam} > {output}"
SnakeMake SAMtools From line 154 of rules/samtools.smk
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/CBIbigA/ChIP-seq
Name: chip-seq
Version: 2
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Other Versions:
Version Version 1
Downloaded: 0
Copyright: Public Domain
License: MIT License
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