add script to prep data

utils/prep_course_data.sh

@@ -0,0 +1,88 @@
+#!/bin/bash
+
+#### ChIP-seq ####
+
+# chipseq
+wget -O chipseq_reads.zip "https://www.dropbox.com/scl/fo/z4cmuve1w1d35xua1nd9v/AKCbsPVoFv9RK4taeR4wKrQ?rlkey=dz1cqnwjf4rhktxu5nur9xg8u&st=wcf8tvmr&dl=1"
+unzip chipseq_reads.zip -d chipseq
+
+wget -O chipseq_genome.zip "https://www.dropbox.com/scl/fo/3jdyj7sivv4krsdfca2kn/AGMtbP0zvsF5RWa8uZSBL4E?rlkey=jxezn2xpyb999swrphrhpdguq&st=8mjwzjd0&dl=1"
+unzip chipseq_genome.zip -d chipseq/genome/
+
+wget -O chipseq_samplesheet.csv "https://www.dropbox.com/scl/fi/qxgovzlnbmyz211e5snw4/samplesheet.csv?rlkey=ktznsllql56ropxkk78owy6ov&st=gfxavb20&dl=1"
+cat chipseq_samplesheet.csv | cut -d , -f 2,1,4,5 | sed 's/sample,fastq_1,antibody,control/name,fastq,antibody,input_control/' | sed 's|data/reads/||' | sed 's/.fastq.gz//' | tr ',' '\t' > chipseq/sample_info.tsv
+
+rm chipseq/genome/GRCh38.109.chrom_sizes.tsv chipseq/genome/GRCh38.109.gtf.gz chipseq/genome/degs_nagarajan2017.csv
+
+
+#### RNA-seq ####
+
+# rnaseq - reads
+wget -O rnaseq_reads.zip "https://www.dropbox.com/scl/fo/8c1rls797tydp05yofogq/AILyg8jk1UyN6L_7VgSAIqM?rlkey=faa0k56me69ceaev3k06fewi8&st=203t82j4&dl=1"
+unzip rnaseq_reads.zip -d rnaseq
+
+mv rnaseq/fastq rnaseq/reads
+cat rnaseq/samplesheet.tsv | sed 's/SampleName/fastq/' > rnaseq/sample_info.tsv
+rm rnaseq/nextflow_samplesheet.csv rnaseq/samplesheet.tsv rnaseq/samplesheet_corrected.tsv
+# I've done further modifications to sample_info.tsv manually
+
+# genome
+mkdir rnaseq/genome
+wget -O rnaseq/genome/Mus_musculus.GRCm38.dna_sm.chr14.fa.gz "https://www.dropbox.com/scl/fi/4ic0mfpw5ol4l5nkrj7fb/Mus_musculus.GRCm38.dna_sm.chr14.fa.gz?rlkey=btiaaistbdyydzo8gbp1tf6vp&st=x6gw457j&dl=1"
+wget -O rnaseq/genome/Mus_musculus.GRCm38.102.chr14.gtf.gz "https://www.dropbox.com/scl/fi/t15rzrf00u243lgzi4c1w/Mus_musculus.GRCm38.102.chr14.gtf.gz?rlkey=3a926xzw97o3jh80sdd5jf173&st=nnojx33j&dl=1"
+
+
+#### Virus ####
+
+# viralrecon illumina
+wget -O sars_illumina.zip "https://www.dropbox.com/scl/fo/lbw1eucabhrd26ce4xf1j/h?rlkey=aelkvldj1hta8xaqnqzkydb7v&st=uwhar7jf&dl=1"
+unzip sars_illumina.zip -d virus_illumina
+
+mv virus_illumina/data/reads virus_illumina/reads
+cat virus_illumina/samplesheet.csv | cut -d , -f 1,2 | sed 's/sample,fastq_1/name,fastq/' | sed 's|data/reads/||' | sed 's/_1.fastq.gz//' | tr ',' '\t' > virus_illumina/sample_info.tsv
+rm -r virus_illumina/data virus_illumina/resources virus_illumina/scripts virus_illumina/samplesheet.csv virus_ont/sample_info.csv
+
+mkdir virus_illumina/genome
+wget -O virus_illumina/genome/nCoV-2019.reference.fasta "https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta"
+wget -O virus_illumina/genome/nCoV-2019.annotation.gff.gz "https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz"
+wget -O virus_illumina/genome/nCoV-2019.V3.primer.bed "https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed"
+
+
+# viralrecon ONT
+wget -O sars_ont.zip "https://www.dropbox.com/scl/fo/y37yqean6vamzr7yq8zey/h?rlkey=qdavkteytx8inv0qpvai11lby&st=8lcnf9w8&dl=1"
+unzip sars_ont.zip -d virus_ont
+
+mv virus_ont/data/fastq_pass virus_ont/fastq_pass
+cat virus_ont/samplesheet.csv | sed 's/sample,barcode/name,ont_barcode/' | tr ',' '\t' > virus_ont/sample_info.tsv
+rm -r virus_ont/data virus_ont/resources virus_ont/scripts virus_ont/samplesheet.csv virus_ont/sample_info.csv
+
+mkdir virus_ont/genome
+wget -O virus_ont/genome/nCoV-2019.reference.fasta "https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta"
+wget -O virus_ont/genome/nCoV-2019.annotation.gff.gz "https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz"
+wget -O virus_ont/genome/nCoV-2019.V3.primer.bed "https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed"
+
+
+#### Bacteria ####
+
+# not doing this as it requires several databases, which seems overkill
+
+# # vibrio illumina
+# for sra in ERR1485225 ERR1485227 ERR1485229 ERR1485231
+# do
+#   # prefetch
+#   prefetch ${sra}
+
+#   # validate
+#   vdb-validate ${sra}
+
+#   # convert
+#   fasterq-dump --outdir  temp/ ${sra}
+
+#   # subsample to 10% and gzip
+#   cat temp/${sra}_1.fastq | seqtk sample -s 1 - 0.1 | gzip > reads/${sra}_1.downsampled.fastq.gz
+#   cat temp/${sra}_2.fastq | seqtk sample -s 1 - 0.1 | gzip > reads/${sra}_2.downsampled.fastq.gz
+
+#   rm -r ${sra} temp
+# done
+
+