Hi,

I need to analyze down-sampled data of couple of Rna_Seq full data set (samples,paired-end,fastq).sub-sampling method should work the same for all samples. In the end I compare for example how 5% of full data differs from 10% of full and 20 and 40% as well. (a sample is :ERR188044)
The final graph will depict how amount of data affects the result.

The question is :
How to download the data in these four forms ? shall I firstly download the full data and then downsample ? Or I can directly download down-sampled data.
how to sub-sample data to get only a few number of specific chromosomes ?
how to sub-sample data to get only a percent of whole paired-end reads?

What do you suggest me to do ?

Your advice is appreciated.

Thanks. 
FYI, the term you're looking for to describe this is a "rarefaction curve".

Yes, you will need to download the full dataset and then subsample it (typically a few times) for each percentage you want to plot on the X axis. You can use things like `seqtk` or even `samtools view` to subsample files. Depending on what you need to do, aligning the whole dataset once and then subsampling that will likely turn out to be the quickest strategy.