When to run fastq-dump --split-files -X 10000 ?

Question

[akshay_ware]

I am doing RNA-Seq data analysis of SRA data. I am not understanding the purpose of command

fastq-dump --split-files -X 10000

Why to split file? and if i don't know the data is paired end or single end. is there is need to use -X 10000 ?

Thanks in advance

Answer 1

[Devon Ryan]

If you always use --split-files then you never have to worry about forgetting to use it with PE data. There is no reason to use -X 10000 unless you just want a subset of the reads for testing something quicker.