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Prepare Sample Sheet

To automatically generate FASTQ files from the run folder using BaseSpace Sequence Hub, you must create a sample sheet prior to initiating a sequencing run.

• The following sample sheet templates are provided on the Illumina support website.
• For sequencers that use standard i5 primer notation
• For sequencers using reverse complemented i5 primer notation

For more information, refer to the Indexed Sequencing Overview Guide on the Illumina support website.

• The sample sheet templates contain the following parameters that are required for processing by the UMI Error Correction Software.
• Read1UMILength 7
• Read2UMILength 7
• Read1StartFromCycle 9
• Read2StartFromCycle 9
• If you are using a sample sheet within the run folder, the sample sheet must be named SampleSheet.csv.
• Reads section must be defined.
• Maximum number of samples per analysis run is 48.
• Data section—required columns and column headers are as follows.
• Sample_ID
• Sample_Name
• Index
• Index2

NOTE

HiSeq 4000 uses reverse complements of the second index (i5).

• Sample ID is used in output file names instead of the sample name. For an easier transition between the UMI Error Correction BaseSpace Sequence Hub App and the UMI Error Correction Local App (without changing the file name), do not use underscores in Sample IDs and leave the Sample Name blank.
• Sample_ID naming conventions are as follows.
• Alphanumeric, length less than 100 characters
• Cannot contain nonalphanumeric special characters (* . " / \ [ ] : ; | = ,), spaces, or characters reserved by BaseSpace (_)
• It is recommended that you prefix Sample_IDs with a keyword
• Unique Combinations of Sample_ID and Lane Number

CAUTION

Sample_Name and Sample_ID cannot contain underscore characters (_). Underscores cause issues during secondary analysis.

• Lane Number
• Do not use 1+2+3+4 naming convention to specify multiple lane usages when uploading data to BaseSpace Sequence Hub. Instead specify sample and lanes individually or leave the lane column blank to indicate all lanes.