forked from GRIAC/system_genetics
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step3/star
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p280381-fe
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#!/bin/bash
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#
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# Align reads against reference genome.
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STORAGE="/groups/umcg-griac/tmp04/rawdata/$(whoami)/step3"
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# Store genome index in this location:.
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GENOME_INDEX="${STORAGE}/genome_index"
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mkdir -p "${GENOME_INDEX}"
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# Store the generated `Aligned.sortedByCoord.out.bam` in this dir.
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ALIGNMENT_OUTPUT="${STORAGE}/alignment"
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mkdir -p "${ALIGNMENT_OUTPUT}"
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# 1) Generate genome index.
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#
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# N.B.:
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# - We're assuming a read size of 100 bp (--sjdbOverhang 100). Refer back to the
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# previous quality control steps if you are unsure about the size. In case of
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# reads of varying length, the ideal value is max(ReadLength)-1.
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# - We're using gzip compressed reference data (--readFilesCommand zcat), i.e.,
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# .gtf.gz and fa.gz. If not, you can remove the `zcat` flag.
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# Storage location reference data (in this case on calculon).
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REFERENCE_DATA="/groups/umcg-griac/prm02/rawdata/reference/genome"
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GTF_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.100.gtf.gz"
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FASTA_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
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STAR \
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--runThreadN 8 \
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--runMode genomeGenerate \
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--readFilesCommand zcat \
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--sjdbOverhang 100 \
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--genomeFastaFiles ${FASTA_FILE} \
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--sjdbGTFfile ${GTF_FILE} \
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--genomeDir ${GENOME_INDEX}
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# 2) Do the actual alignment.
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#
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# N.B.:
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# - We are assuming paired-end, gzip compressed (--readFilesCommand zcat) FastQ
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# files.
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# THe compressed paired-end FastQ's that we are aligning.
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R1="sample1_R1.fastq.gz"
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R2="sample1_R2.fastq.gz"
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STAR \
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--runThreadN 8 \
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--readFilesCommand zcat \
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--readFilesIn "${R1}" "${R2}" \
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--outSAMtype BAM SortedByCoordinate \
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--genomeDir ${GENOME_INDEX} \
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--outFileNamePrefix "${ALIGNMENT_OUTPUT}"
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18
rnaseq/step5_count/snippet_counts
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18
rnaseq/step5_count/snippet_counts
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## Generate Raw Counts using FeatureCounts/HTSeqCounts
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## Load package Subread (packge within which FeatureCounts is present)
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+ ml Subread/1.6.4-foss-2015b FeatureCounts
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## Features used in FeatureCounts :
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## -s : reversely stranded
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## -T : number of threads used
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## -a : reference genome
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## -o : output file
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+ featureCounts \
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+ --a "path to reference genome" \
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+ --T 6 \
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+ --o "path to output file" \
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+ --s 2
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