upload bam files to Basespace

[Nital Shah]

Hi,

My algorithm takes input as bam files but in Basespace we can only input FastQ, vcf and manifest(also need to knw what this "Manifest" is!!)

The documentation says that user can input bam files that were in App Results.

So can i make an app that allows only bam files as input, or should i also provision for fastQ?

Thanks,

Nital

[Mayank Tyagi]

Hey Nital,

Both bam files and fastq files are available to apps.  You can use the FileChooser in the input form for the app to allow the user to select .bam files within their account.  If the app runs on .bam files, I would recommend using the FileChooser with an 'extensionFilters' value of '.bam' to ensure that only .bam files are shown. 

Please let us know if you run into any issues with the above.

Sincerely,

The BaseSpace Platform Team