BaseSpace says NextSeq run finished, can't download FastQ

Question

[Adrian Pelin]

Hello,

My Sequencing provider shared the run on BaseSpace with me on Friday, and now that the run is completed on Saturday, I want to download the reads. The run even has "FastQ Generation" App that ran and extracted FastQ reads for all samples that were indexed, and I can see the amount of reads, but I cannot download it (it does not allow me to click on "Download FastQ files").

I was able to download the BCL files, but when I am converting them to FastQ all reads end up Undetermined and I do not know what the index sequences are.

This is a NextSeq system.

Did anyone run into anything like this?

[John]

Contact your sequencing provider :) They may have messed up the sharing permissions.

[Adrian Pelin]

Okay, I found this info about indexes. So the first sample had "TAAGGCGA+TCTTACGC". Any idea how I can demultiplex this from bcl using bcl2fastq2? There must be a way to write a sample sheet with all these indexes.

Answer 1

[igor]

To download the FASTQ files, the provider has to also share the project with you. BaseSpace has "runs" that contain run metrics and some raw files. The "projects" contain the demultiplexed samples. The project is not available until the run is completed and can only be shared at that point, which may be why they did not share that with you on Friday.

[Adrian Pelin]

Makes perfect sense. The run had information on the index sequences used, so I ended up creating a sample sheet and extracting FastQ files myself using the index sequences shown.