Commit b9218a01 authored by JihedC's avatar JihedC
Browse files

removed unnecessary files

parent bab1a3b4
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
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GL456211.1 241735
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GL456213.1 39340
GL456216.1 66673
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GL456239.1 40056
GL456350.1 227966
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GL456360.1 31704
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GL456368.1 20208
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GL456392.1 23629
GL456393.1 55711
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GL456396.1 21240
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JH584304.1 114452
rule mapping:
input:
forward_reads = WORKING_DIR + "trimmed/{samples}_forward.fastq.gz",
reverse_reads = WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz",
forwardUnpaired = WORKING_DIR + "trimmed/{samples}_forward_unpaired.fastq.gz",
reverseUnpaired = WORKING_DIR + "trimmed/{samples}_reverse_unpaired.fastq.gz",
index = [WORKING_DIR + "genome." + str(i) + ".bt2" for i in range(1,4)]
output:
mapped = WORKING_DIR + "mapped/{samples}.bam",
unmapped = [WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)],
params:
bowtie = " ".join(config["bowtie2"]["params"].values()), #take argument separated as a list separated with a space
index = WORKING_DIR + "genome",
unmapped = WORKING_DIR + "unmapped/{samples}.fq.gz"
threads: 10
conda:
"../envs/samtools_bowtie.yaml"
log:
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}
"""
# -x <bt2-idx> The basename of the idex for the reference genome. The basename is the name of any of the index files up to but not including the final (.1.bt2; rev.1.bt2 etc)
# -1 comma-separated list of forward reads files
# -2 comma-separated list of reverse reads files
# -U comma-separated list of files containing unpaired reads to be aligned.
# output options: --un-gz <path> write unpaired reads that failed to align concordantly to file at <path>, and will be gzip comppressed.
#samtools view -Sb: convert SAM format to BAM format.
Functions of samtools:
1. convert from other alignment formats
2. sort and merge alignments
3. label PCR duplicates
4. call SNP and short indel variants
5. show alignments in text-based viewer
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