Introduction to Data Acquisition

What is Data Acquisition?

Data acquisition is how data is obtained through the process of downloading or transferring files from one location to another. In this section of the bioinformatics workbook, we will discuss the unix commands used to transfer/download data and also the web repositories to which data is deposited and from which data can be downloaded.

Learning Objective

Upon completion of this section on experimental design the learner will be able to:

Index

• File Transfer
  • File Transfer using wget
  • File Transfer using Globus
  • File Transfer using irods
  • File Transfer using SRA toolkit
• Data Sets Used in the tutorials
• FASTA manipulation
  • Determining Sequence length
  • Converting FastQ to FASTA
  • FASTQ Quality trimming
  • Retrieving FASTA file using sequence ID
• Manipulating Excel data sheets
  • Create Workbook from Multiple Text Files
  • Export multiple worksheets as separate text files
  • Create Index for All Worksheets
  • Merge two spreadsheets using a common column
• Data Management
  • Deposition of Data to NCBI SRA
  • Deposition of raw data to ENA
  • Deposition of Genome to ENA

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