Requirements for uploading FASTQ Files to BaseSpace via web interface

By default, any FASTQ files generated from Illumina software using the default settings can be uploaded to BaseSpace Sequence Hub without the need to manipulate information to upload them to BaseSpace. If the FASTQ files are generated in a non-standard way, use the following naming convention for the file names. SampleName_SampleNumber_Lane_Read_FlowCellIndex.fastq.gz

The SampleName cannot contain any underscores. If present, they must either be deleted or changed to the dash character (eg, Sample_1 to Sample-1). Additionally, the read headers/descriptors within the FASTQ file must following a similar convention. @Instrument:RunID:FlowCellID:Lane:Tile:X:Y ReadNum:FilterFlag:0:SampleNumber

The Lane value is different if FASTQ files are merged from multiple lanes (eg, by using bcl2fastq with --no-lane-splitting). If this is the cased, the data must be reprocessed using lane splitting (default setting) to proceed with uploading to BaseSpace.

Additional considerations for uploading to BaseSpace:* FASTQ files for index reads cannot be uploaded along with R1 and R2 FASTQ files.

• R2 FASTQ files cannot be uploaded without R1.

• FASTQ files with containing reads that did not pass filter (ie, non-PF reads; eg, FilterFlag is Y in FASTQ Header) cannot be uploaded.

• Only a single sample can be uploaded per upload session and the total file size cannot exceed 25 GB.

• Illumina recommends a minimum 10 MB/s upload speed to avoid any uploads from timing out.

Refer to the FASTQ File Upload Requirements page for additional information.

Note: BaseSpace Command Line Interface (CLI) can be used to upload lane merged FASTQ files and FASTQ files for multiple samples at a time. For more information, search for Knowledge Base article How to upload FASTQ files to BaseSpace with BaseSpace CLI.

For any feedback or questions regarding this article (Illumina Knowledge Article #1313), contact Illumina Technical Support [e-mail].