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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 page for additional information.

To upload compatible fastq files to BaseSpace via the web interface:

Navigate to the project to which the fastq files will be uploaded.
Near the top left, under the project name, select the File icon (which looks like a piece of paper with the corner folded), then select Upload > Files.
Select the FASTQ radio button under the Choose File Type section.
In the Select and Review section, either browse to the file(s) to be uploaded, or drag and drop the files to be uploaded to the upload section.
- Note: files can only be uploaded for one sample at a time, and it is important to upload all files for one sample in a single upload event.
In the third Complete Upload section, select to save the upload to a Sample or Biosample, select the Biosample; if relevant, add the library name in the free text field; and select the Library Prep Kit used from the dropdown menu (optional), then select Complete Upload.
- Note: it is possible to select the Complete Upload option before the fastq files have completed import; the page will complete the process when the upload process completes.

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.

Last updated 17 days ago

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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 page for additional information.

To upload compatible fastq files to BaseSpace via the web interface:

Navigate to the project to which the fastq files will be uploaded.
Near the top left, under the project name, select the File icon (which looks like a piece of paper with the corner folded), then select Upload > Files.
Select the FASTQ radio button under the Choose File Type section.
In the Select and Review section, either browse to the file(s) to be uploaded, or drag and drop the files to be uploaded to the upload section.
- Note: files can only be uploaded for one sample at a time, and it is important to upload all files for one sample in a single upload event.
In the third Complete Upload section, select to save the upload to a Sample or Biosample, select the Biosample; if relevant, add the library name in the free text field; and select the Library Prep Kit used from the dropdown menu (optional), then select Complete Upload.
- Note: it is possible to select the Complete Upload option before the fastq files have completed import; the page will complete the process when the upload process completes.

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