How to generate a Sample Sheet from sample/index data in BaseSpace

If you are using BaseSpace for sample entry but demultiplexing your data manually, you may have been frustrated that there is no facility to download your sample names and index tag data from BaseSpace as a sample sheet. This means you have to enter the same data twice – with the possibility of errors creeping in especially for large projects with many samples and dual index tags.

We have found a way to avoid typing the same information twice and instead fetch the sample names, index ID’s and index tag sequences from BaseSpace straight to a sample sheet. This saves a huge amount of time for large projects with many samples.

Log in to BaseSpace, and navigate to the ‘Libraries’ page within the ‘Prep Libraries’ tab. Each line is a set of libraries with complete information on index names and tag sequences. Clicking a set of libraries will bring up the following screen – this example has 24 samples with TruSeqLT tags (only 7 are visible without scrolling down the list).


Clicking the ‘EXPORT’ button will download a comma separated file (csv) that can be opened in Excel. This file has all the sample names, index ID’s and index sequences (but not in quite the correct format to paste into a sample sheet).


Open the file in Excel, select the entire Index1 Column and click the ‘Text to Columns’ function (under the ‘Data’ menu in Excel). Choose the ‘Delimited’ option, then tick ‘Other’ and enter a hyphen (-) in the box. This will split the Index1 Column into two, with the name of the Index and the actual Tag sequence in two separate columns, as below.


If using dual indexing (e.g. TruSeqHT or NexteraXT) then do the same for the second column with Index 2 to split the index2 names and sequences into two separate columns.

Now open a blank or used sample sheet that is set up for the correct library chemistry and sequencing instrument (see previous blog post) then copy and paste the sample ID’s, Index ID’s and Index sequences into the sample sheet. Save as a comma separated file (csv) and its ready to use for demultiplexing and fastq generation, or your next MiSeq run. The above example looks like this…