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Commit 8269c82d authored by WJH58's avatar WJH58
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added params under rule peak_calling

parent c0085bb1
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ATAC-seq_pipeline/NA.log 0 → 100644
View file @ 8269c82d
Version: 1.2.10
Arguments Used:
-b temp/sort/WT8.sorted.bam
-i temp/index/WT8.sorted.bam.bai
-g genome.info
ATAC-seq_pipeline/WT8.log 0 → 100644
View file @ 8269c82d
Version: 1.2.10
Arguments Used:
-b temp/sort/WT8.sorted.bam
-i temp/index/WT8_map.sorted.bam.bai
-g genome.info
--output WT8
--upper 20
--lower 10
ATAC-seq_pipeline/config.yaml
View file @ 8269c82d
......@@ -35,3 +35,7 @@ bowtie2:
max_fragment_len: "--maxins 500" # maximum fragment length for valid paired-end alignments
min_fragment_len: "--minins 80" # minimum fragment length for valid paired-end alignments
verbose: "-q"
# genome.info
hmmratac:
genome.info: "genome.info"
ATAC-seq_pipeline/envs/hmmratac.yaml 0 → 100644
View file @ 8269c82d
channels:
- bioconda
dependencies:
- HMMRATAC=1.2.10
ATAC-seq_pipeline/envs/perl.yaml 0 → 100644
View file @ 8269c82d
channels:
- bioconda
dependencies:
- perl-bioperl=1.7
- samtools=1.9
ATAC-seq_pipeline/genome.info 0 → 100644
View file @ 8269c82d
chr1 195471971
chr2 182113224
chr3 160039680
chr4 156508116
chr5 151834684
chr6 149736546
chr7 145441459
chr8 129401213
chr9 124595110
chr10 130694993
chr11 122082543
chr12 120129022
chr13 120421639
chr14 124902244
chr15 104043685
chr16 98207768
chr17 94987271
chr18 90702639
chr19 61431566
chrX 171031299
chrY 91744698
chrM 16299
GL456210.1 169725
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GL456216.1 66673
GL456219.1 175968
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GL456233.1 336933
GL456239.1 40056
GL456350.1 227966
GL456354.1 195993
GL456359.1 22974
GL456360.1 31704
GL456366.1 47073
GL456367.1 42057
GL456368.1 20208
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JH584304.1 114452
ATAC-seq_pipeline/labjournal/19-11-2020.md deleted 100644 → 0
View file @ c0085bb1
```
rule trimmomatic:
input:
reads = get_fastq,
adapters = config['trimmomatic']["adapters"]
output:
forward_reads = WORKING_DIR + "trimmed/{samples}_forward.fastq.gz",
reverse_reads = WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz",
forwardUnpaired = temp(WORKING_DIR + "trimmed/{samples}_forward_unpaired.fastq.gz"),
reverseUnpaired = temp(WORKING_DIR + "trimmed/{samples}_reverse_unpaired.fastq.gz"),
log:
RESULT_DIR + "logs/trimmomatic/{samples}.log"
params:
seedMisMatches = str(config['trimmomatic']['seedMisMatches']),
palindromeClipTreshold = str(config['trimmomatic']['palindromeClipTreshold']),
simpleClipThreshhold = str(config['trimmomatic']['simpleClipThreshold']),
LeadMinTrimQual = str(config['trimmomatic']['LeadMinTrimQual']),
TrailMinTrimQual = str(config['trimmomatic']['TrailMinTrimQual']),
windowSize = str(config['trimmomatic']['windowSize']),
avgMinQual = str(config['trimmomatic']['avgMinQual']),
minReadLen = str(config['trimmomatic']['minReadLength']),
phred = str(config["trimmomatic"]["phred"])
threads: 10
conda:
"envs/trimmomatic.yaml"
shell:
"""
trimmomatic PE \
-threads 10 \
-phred33 \
{input.reads} \
{output.forward_reads} {output.forwardUnpaired} {output.reverse_reads} {output.reverseUnpaired} \
ILLUMINACLIP:{input.adapters}:{params.seedMisMatches}:{params.palindromeClipTreshold}:{params.simpleClipThreshhold} \
LEADING:3 \
TRAILING:3 \
SLIDINGWINDOW:4:15 \
MINLEN:40 &>{log}
"""
```
####Trimmomatic Arguments####
ATAC-seq_pipeline/results/peaks/WT8_peaks.gappedPeak.log 0 → 100644
View file @ 8269c82d
Version: 1.2.10
Arguments Used:
-b temp/sort/WT8.sorted.bam
-i temp/index/WT8_map.sorted.bam.bai
-g genome.info
--output results/peaks/WT8_peaks.gappedPeak
--upper 20
--lower 10
ATAC-seq_pipeline/snakefile
View file @ 8269c82d
......@@ -50,7 +50,9 @@ TRIMMED_FASTQC = expand(RESULT_DIR + "trimmed_fastqc/WT8_{direction}_fastqc.htm
MAPPED = expand(WORKING_DIR + "mapped/{samples}.bam", samples = SAMPLES),
UNMAPPED = expand([WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)], samples = SAMPLES),
MAP_SORTED = expand(WORKING_DIR + "sort/{samples}.sorted.bam", samples = SAMPLES),
SORTED_INDEXED = expand(WORKING_DIR + "index/{samples}.sorted.bam.bai", samples = SAMPLES)
SORTED_INDEXED = expand(WORKING_DIR + "index/{samples}.sorted.bam.bai", samples = SAMPLES),
GENOME_INFO = expand(WORKING_DIR + "genome_info/{samples}.genome.info", samples = SAMPLES),
GAPPED_PEAK = expand(RESULT_DIR + "peaks/{samples}_peaks.gappedPeak", samples = SAMPLES)
rule all:
input:
......@@ -65,7 +67,9 @@ rule all:
MAPPED,
UNMAPPED,
MAP_SORTED,
SORTED_INDEXED
SORTED_INDEXED,
GENOME_INFO,
GAPPED_PEAK
message : "Analysis is complete!"
shell:""
......@@ -180,29 +184,64 @@ rule mapping:
RESULT_DIR + "logs/bowtie/{samples}.log"
shell:
"""
bowtie2 {params.bowtie} --threads {threads} -x {params.index} -1 {input.forward_reads} -2 {input.reverse_reads} -U {input.forwardUnpaired},{input.reverseUnpaired} --un-conc-gz {params.unmapped} | samtools view -Sb - > {output.mapped} 2>{log}
bowtie2 {params.bowtie} --threads {threads} -x {params.index} -1 {input.forward_reads} -2 {input.reverse_reads} -U {input.forwardUnpaired},{input.reverseUnpaired} --un-conc-gz {params.unmapped} | samtools view -Sb - > {output.mapped} 2>&{log}
"""
rule sort:
input:
mapped = WORKING_DIR + "mapped/{samples}.bam"
output:
map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
map_sorted = WORKING_DIR + "sort/{samples}_map.sorted.bam"
conda:
"envs/samtools_bowtie.yaml"
log:
RESULT_DIR + "logs/sort/{samples}.log"
shell:
"samtools sort {input} -o {output}"
"samtools sort {input} -o {output} &>{log}"
rule index:
input:
map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
map_sorted = WORKING_DIR + "sort/{samples}_map.sorted.bam"
output:
sorted_indexed = WORKING_DIR + "index/{samples}.sorted.bam.bai"
map_sorted_indexed = WORKING_DIR + "index/{samples}_map.sorted.bam.bai"
conda:
"envs/samtools_bowtie.yaml"
log:
RESULT_DIR + "logs/index/{samples}.log"
shell:
"samtools index {input} {output}"
"samtools index {input} {output} &>{log}"
rule get_genome_info:
input:
map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
output:
genome_info = WORKING_DIR + "genome_info/{samples}.genome.info"
conda:
"envs/perl.yaml"
shell:
"""
samtools view -H {input} | grep SQ | cut -f 2-3 | cut -d ':' -f 2 | cut -f 1 > tmp
samtools view -H {input} | grep SQ | cut -f 2-3 | cut -d ':' -f 2,3 | cut -d ':' -f 2 > tmp2
paste tmp tmp2 > {output}
rm tmp tmp2
"""
rule peak_calling:
input:
map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam",
map_sorted_indexed = WORKING_DIR + "index/{samples}_map.sorted.bam.bai"
output:
gapped_peak = RESULT_DIR + "peaks/{samples}_peaks.gappedPeak"
params:
genome_info = str(config['hmmratac']['genome.info']),
upper = 20,
lower = 10,
output_preflix = "{samples}"
log:
RESULT_DIR + "logs/peak_calling/{samples}.log"
conda:
"envs/hmmratac.yaml"
shell:
"""
HMMRATAC -b {input.map_sorted} -i {input.map_sorted_indexed} -g {params.genome_info} --output {params.output_preflix} --upper {params.upper} --lower {params.lower} 2&>{log}
"""
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