How to download bulk fastq data for Analysis Pipeline

[rajeev.vikram]

Hi,

I am looking for tutorial or step by step guide to download RNA-Seq data in bulk from DBs like GEO/SRA or Encode and directly put it in the analysis pipeline. (A kind of automated system which runs when initiated by direct data feed.

If anyone could help, it would be really great.

Thanks.

[InDel]

For data from public database, you always need to do data quality check to make sure you get the right input for your pipeline.