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Adding scripts, and associated data to reproduce the case studies use…
…d in our manuscript. Also contains two example visualizations
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CaseStudy/ExampleVisualization/Visualization_BasicStatistics_rDNA_EST_51A.html
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CaseStudy/ExampleVisualization/Visualization_Comparison_All_rDNA.html
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| ################################################################################################## | ||
| # # | ||
| # Script for the case studies in manuscript "Automated analysis of small RNA datasets with RAPID"# | ||
| # Karunanithi et. al., # | ||
| # # | ||
| # This script assumes you have the following softwares installed and in PATH: # | ||
| # conda # | ||
| # cutadapt (v1.8.1) # | ||
| # trim_galore # | ||
| # RAPID as a condo env (see https://rapid-doc.readthedocs.io/en/latest/Installation.html) # | ||
| # # | ||
| # This script reproduces the analysis done in this manuscript and it # | ||
| # reproduces figures (except Fig.1). # | ||
| # # | ||
| # # | ||
| # RUN THE SCRIPT IN THE FOLDER WHERE YOU HAVE ALL ASSOCIATED SUPPLEMENTARY FILES DOWNLOADED # | ||
| # # | ||
| # UPDATE THE CONDA ENVIRONMENT VARIABLE FOR RAPID BELOW # | ||
| # # | ||
| ################################################################################################## | ||
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| ENV_NAME=<environment_name> | ||
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| ####################################################### Data Download, and Preprocessing | ||
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| ### Paramecium tetraurelia related | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/ERR250/000/ERR2503570/ERR2503570.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/ERR250/001/ERR2503571/ERR2503571.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/ERR250/002/ERR2503572/ERR2503572.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/ERR250/003/ERR2503573/ERR2503573.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/ERR250/004/ERR2503574/ERR2503574.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/ERR250/005/ERR2503575/ERR2503575.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/ERR250/006/ERR2503576/ERR2503576.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/ERR250/007/ERR2503577/ERR2503577.fastq.gz | ||
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| # Merge replicates, and rename samples | ||
| cat ERR2503570.fastq.gz ERR2503571.fastq.gz >51A_unfilt.fq.gz | ||
| cat ERR2503572.fastq.gz ERR2503573.fastq.gz >51B_unfilt.fq.gz | ||
| cat ERR2503574.fastq.gz ERR2503575.fastq.gz >51D_unfilt.fq.gz | ||
| cat ERR2503576.fastq.gz ERR2503577.fastq.gz >51H_unfilt.fq.gz | ||
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| # Data trimming | ||
| # The reads are already adapter trimmed. | ||
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| # Filter Reads (you need install cutadapt(v1.8.1) to perform this) | ||
| cutadapt -m 21 -M 25 ./51A_unfilt.fq.gz -o ./51A.fq.gz | ||
| cutadapt -m 21 -M 25 ./51B_unfilt.fq.gz -o ./51B.fq.gz | ||
| cutadapt -m 21 -M 25 ./51D_unfilt.fq.gz -o ./51D.fq.gz | ||
| cutadapt -m 21 -M 25 ./51H_unfilt.fq.gz -o ./51H.fq.gz | ||
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| #Remove raw and intermediate files | ||
| rm *_unfilt.fq.gz ERR250357*.fastq.gz | ||
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| ### Spombe related | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/006/SRR4449666/SRR4449666.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/007/SRR4449667/SRR4449667.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/008/SRR4449668/SRR4449668.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/009/SRR4449669/SRR4449669.fastq.gz | ||
| cat SRR4449* >WT_24h.fq.gz | ||
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| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/000/SRR4449690/SRR4449690.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/001/SRR4449691/SRR4449691.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/002/SRR4449692/SRR4449692.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/003/SRR4449693/SRR4449693.fastq.gz | ||
| cat SRR4449* >ago1D_24h.fq.gz | ||
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| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/004/SRR4449714/SRR4449714.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/005/SRR4449715/SRR4449715.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/006/SRR4449716/SRR4449716.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/007/SRR4449717/SRR4449717.fastq.gz | ||
| cat SRR4449* >clr4D_24h.fq.gz | ||
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| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/008/SRR4449738/SRR4449738.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/009/SRR4449739/SRR4449739.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/000/SRR4449740/SRR4449740.fastq.gz | ||
| wget --no-passive-ftp ftp.sra.ebi.ac.uk/vol1/fastq/SRR444/001/SRR4449741/SRR4449741.fastq.gz | ||
| cat SRR4449* >dcr1D_24h.fq.gz | ||
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| # Adapter trimming, and Read filtering (you need install cutadapt(v1.8.1) to perform this) | ||
| for file in *.fq.gz; | ||
| do | ||
| name=`echo $file|cut -d. -f1`; | ||
| echo ${name}_trimmed.fq.gz; | ||
| trim_galore --length 18 --max_length 25 $file | ||
| mv ${name}_trimmed.fq.gz $file | ||
| done; | ||
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| #Remove raw and intermediate files | ||
| rm SRR4449*.fastq.gz *_trimming_report.txt | ||
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| ### Move in to conda environment | ||
| source activate $ENV_NAME | ||
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| # Build index for rDNA (bowtie2 installation necessary) | ||
| bowtie2-build rDNAcluster.fa rDNAIndex | ||
| bowtie2-build Spombe_ASM294v2.fasta Spombe_ASM294v2 | ||
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| #Run the basic statistics for Paramecium data. | ||
| rapidStats.sh -o=./rDNA_51A/ -f=./51A.fq.gz -a=./rDNAClusterRegions.bed -i=./rDNAIndex | ||
| rapidStats.sh -o=./rDNA_51B/ -f=./51B.fq.gz -a=./rDNAClusterRegions.bed -i=./rDNAIndex | ||
| rapidStats.sh -o=./rDNA_51D/ -f=./51D.fq.gz -a=./rDNAClusterRegions.bed -i=./rDNAIndex | ||
| rapidStats.sh -o=./rDNA_51H/ -f=./51H.fq.gz -a=./rDNAClusterRegions.bed -i=./rDNAIndex | ||
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| #Run the normalisation to compare all serotypes. | ||
| rapidNorm.sh -o=./rDNA_Allnorm/ -c=./rDNA_allsamples.config -a=./rDNAClusterRegions.bed | ||
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| #Run the basic statistics for every Pombe data. | ||
| rapidStats.sh -o=./WT_24h/ -f=./WT_24h.fq.gz -a=./sRNAenrichedGenelist_mmc2.bed -i=./Spombe_ASM294v2 | ||
| rapidStats.sh -o=./ago1D_24h/ -f=./ago1D_24h.fq.gz -a=./sRNAenrichedGenelist_mmc2.bed -i=./Spombe_ASM294v2 | ||
| rapidStats.sh -o=./clr4D_24h/ -f=./clr4D_24h.fq.gz -a=./sRNAenrichedGenelist_mmc2.bed -i=./Spombe_ASM294v2 | ||
| rapidStats.sh -o=./dcr1D_24h/ -f=./dcr1D_24h.fq.gz -a=./sRNAenrichedGenelist_mmc2.bed -i=./Spombe_ASM294v2 | ||
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| #Run the normalisation to compare all serotypes. | ||
| rapidNorm.sh -o=./spombe_Allnorm/ -c=./all_only24h_sRNA.config -a=./sRNAenrichedGenelist_mmc2.bed | ||
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| ######## All Visualisation reports for the data analysed (One sample output is created for each case; uncomment others and run only if necessary, as it might take considerable time) ######### | ||
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| #To create all the comparison plots for Paramecium | ||
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| rapidVis.sh -t=compare -o=./rDNA_Allnorm/ | ||
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| #To create all the plots - Basic statistics of each Paramecium sample | ||
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| rapidVis.sh -t=stats -o=./rDNA_51A/rDNAClusterRegions/ -a=./rDNAClusterRegions.bed | ||
| #rapidVis.sh -t=stats -o=./rDNA_51B/rDNAClusterRegions/ -a=./rDNAClusterRegions.bed | ||
| #rapidVis.sh -t=stats -o=./rDNA_51D/rDNAClusterRegions/ -a=./rDNAClusterRegions.bed | ||
| #rapidVis.sh -t=stats -o=./rDNA_51H/rDNAClusterRegions/ -a=./rDNAClusterRegions.bed | ||
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| #To create all the comparison plots for Pombe | ||
| rapidVis.sh -t=compare -o=./spombe_Allnorm/ | ||
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| #To create all the plots - Basic statistics of each Pombe sample | ||
| rapidVis.sh -t=stats -o=./WT_24h/sRNAenrichedGenelist_mmc2/ -a=./sRNAenrichedGenelist_mmc2.bed | ||
| #rapidVis.sh -t=stats -o=./ago1D_24h/sRNAenrichedGenelist_mmc2/ -a=./sRNAenrichedGenelist_mmc2.bed | ||
| #rapidVis.sh -t=stats -o=./clr4D_24h/sRNAenrichedGenelist_mmc2/ -a=./sRNAenrichedGenelist_mmc2.bed | ||
| #rapidVis.sh -t=stats -o=./dcr1D_24h/sRNAenrichedGenelist_mmc2/ -a=./sRNAenrichedGenelist_mmc2.bed | ||
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| source deactivate |
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