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yk-tanigawa/Makefile to obtain paired-end FASTQ file

Created February 23, 2016 02:12
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Makefile to obtain paired-end FASTQ file
#usage: make SRA=XXXXX.sra
## commands
FASTQ-DUMP = /somewhere/fastq-dump
## files
FASTQ1 = $(SRA:%.sra=%_1.fastq)
FASTQ2 = $(SRA:%.sra=%_2.fastq)
all: $(FASTQ1) $(FASTQ2)
# obtain paired-end fastq files from sra file
$(FASTQ1) $(FASTQ2): $(SRA)
$(FASTQ-DUMP) --qual-filter --split-files $<
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