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get_data.sh
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get_data.sh
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mkdir -p data data/genomes data/rawdata data/results
# wget -r -np -nH --cut-dirs=1 ftp://ftp.flybase.net/releases/FB2017_03/dmel_r6.16/
curl ftp.ensembl.org/pub/release-81/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.81.gtf.gz | gzip -d > data/genomes/BDGP6.Ensembl.81.gtf
curl ftp.ensembl.org/pub/release-81/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna_sm.toplevel.fa.gz | gzip -d > data/genomes/BDGP6.fa
pushd data/rawdata
fastq-dump SRR072893 # male cycle 10 - 848 MB
fastq-dump SRR072903 # male cycle 14D - 730 MB
fastq-dump SRR072905 # female cycle 10 - 985 MB
fastq-dump SRR072915 # female cycle 14D - 860 MB
popd
pushd data/results
wget http://dl.dropboxusercontent.com/u/169950361/SRP004442.stringtie.tar.gz
popd