Downloading Raw Reads

Question

[Jamie]

Hello!

I am trying to do a computational biology project for my school’s science fair and I want to download raw sequencing reads off the SRA database. However these reads are a lot larger than I thought and I’m worried what will happen if my computer runs out of space. How many samples should I have in general for each independent variable? The study has 99 different samples. Should I just buy an external hardrive or something and download all of the files, or could I only use, perhaps, 50 of the 99 samples?

For context I have a MacBook Pro with 1 TB of storage and this is the data that I want to use for my project: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA879084

I’m new to computational biology, so any suggestions would be greatly appreciated!

Answer 1

[ATpoint]

I assume you eventually want counts? Make your life easy and use the counts provided at https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE213092 rather than processing data yourself from scratch, that imo goes beyond a school project.