I am having a go at using sratoolkit for the first time, and wanted to know if the code I am using is appropriate for my data. I am using the same code for multiple different types of sequencing experiments, and am not sure if this is optimal. I'll lay out the sequence types and code below. I think the -3 is irrelevant for the single end data, do not know of any negative consequences of using -3 for Single paired end. I also think there may be a parameter I am missing when applying fastq-dump to miRNA-seq data.
example of code:
./fastq-dump --outdir /fastq --split-3 -I -F -B --skip-technical SRR7663647
This code is being used on the following studies:
Study | Assay Type | Library Layout | Instument
SRP052803 | RNA-seq | PAIRED | Illumina HiSeq 2000
SRP156883 | miRNA-seq | SINGLE | NextSeq 500
SRP156882 | RNA-seq | SINGLE | NextSeq 500
SRP047031 | miRNA-seq | SINGLE | Illumina HiSeq 2000
Any help or advice will be very appreciated.