Download and process data for SRP100604 and SRP268884

Molly Davis added a comment - 22/Nov/22 2:34 PM - edited SRP100604 and SRP268884 have been uploaded and fastq files created. SRA links: https://www.ncbi.nlm.nih.gov/sra?term=SRP100604 https://www.ncbi.nlm.nih.gov/sra?term=SRP268884 Code Example prefetch.slurm #! /bin/bash #SBATCH --job-name=prefetch_SRR #SBATCH --partition=Orion #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --mem=4gb #SBATCH --output=%x_%j.out #SBATCH --time=24:00:00 cd /nobackup/tomato_genome/alt_splicing/SRP100604 module load sra-tools/2.11.0 vdb-config --interactive files=( SRR5279858 SRR5279875 SRR5279883 SRR5280323 SRR5280370 SRR5280382 SRR5280383 SRR5280392 SRR5282476 SRR5282478 SRR5282480 SRR5282481 ) for f in "${files[@]}" ; do echo $f; prefetch $f; done fasterdump.slurm #! /bin/bash #SBATCH --job-name=fastqdump_SRR #SBATCH --partition=Orion #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --mem=40gb #SBATCH --output=%x_%j.out #SBATCH --time=24:00:00 #SBATCH --array=1-12 #setting up where to grab files from file=$(sed -n -e "${SLURM_ARRAY_TASK_ID}p" /nobackup/tomato_genome/alt_splicing/SRP100604/Sra_ids.txt) cd /nobackup/tomato_genome/alt_splicing/SRP100604 module load sra-tools/2.11.0 echo "Starting faster-qdump on $file" ; cd /nobackup/tomato_genome/alt_splicing/SRP100604/$file fasterq-dump ${file}.sra perl /projects/tomato_genome/scripts/validateHiseqPairs.pl ${file}_1.fastq ${file}_2.fastq cp ${file}_1.fastq /nobackup/tomato_genome/alt_splicing/SRP100604/${file}_1.fastq cp ${file}_2.fastq /nobackup/tomato_genome/alt_splicing/SRP100604/${file}_2.fastq echo "finished" Comments on results Directory: /nobackup/tomato_genome/alt_splicing/SRP100604 SRP100604: There were some SRR files that were not double stranded but were single stranded so it could not make _1.fastq and _2.fastq files. List of those SRR's- SRR5282476 SRR5282478 SRR5282480 SRR5282481 Directory: /nobackup/tomato_genome/alt_splicing/SRP268884 SRP268884: Produces all double stranded _1.fastq and _2.fastq files. Next Step: Run Nextflow rnaseq/nf-core pipeline on SRP268884. Question: Should we still use SRP100604 if it contains single stranded SRR files or just use the double stranded files that it contained? [~aloraine] aloraine's answer to the above query: Go ahead and use all the available data in SRP100604. I believe that nextflow is able to handle this complication intelligently. I think you can omit the "second" file name in the "samples" file for single end runs. (Please note that "single strand" is not the same thing as "single end" - make sure that we are talking about the same thing before proceeding.)