Preparing the sample sheet

Make the sample sheet on your personal computer

The sample sheet is a document that allows you to rename the samples with a meaningful and easily recognisable name than the sequencing I.D.

To make the sample sheet:

  1. Open a new spreadsheet document on your personal computer, for example, in MS Excel.
  2. Populate the first column with the unique identification code given to each sample by the sequencing facility.
  3. Populate the second column with a name that is meaningful to you and will be easily recognisable during downstream analysis. The characters can be letters, numbers or ‘_’.
  4. Save the spreadsheet as index_YYYY-MM-DD.csv, substituting YYYY-MM-DD for today's date.

Example sample sheet saved as index_2022-04-29.csv:

AB_PS_1_S1 MTD1_4053D
AB_PS_2_S2 MTD1_DSM
AB_PS_3_S33 PJB1
AB_PS_4_S86 FYS77

In this case there are four samples. The names given by the sequencing facility start AB_PS_.

Important

  • The sample sheet does not have a header row.
  • 1 row = 1 sample.
  • It must be saved in comma separated value (.csv) format.

Finding the unique identification code

The unique identification code used by the sequencing facility is the first part of the sample's name. Remember, there are two files per sample.

For example, if your file pairs are named AB_PS_1_S1_R1_001.fastq.gz and AB_PS_1_S1_R2_001.fastq.gz enter AB_PS_1_S1, ignoring _R1_001.fastq.gz and _R2_001.fastq.gz.

Upload the sample sheet to the Core

Upload (drag and drop) index_YYYY-MM-DD.csv into the Core input directory:

/Core/input_core

A folder with your raw data is also saved here.

Tip

For each sequencing run you will deposit one index file, index_YYYY-MM-DD.csv, and one directory containing the raw read data, YYYY-MM-DD/.

The Core is now ready to run.