This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How do I access statistics for read counts after demultiplexing in bcl2fastq?

I have recently done some demultiplexing in bcl2fastq - however, how can I get data to tell me how many reads were sorted for each index? On basespace a graphical result is given for the total number of reads that passed a qc30. Is there a similar analysis in bcl2fastq?

bcl2fastq
• 3,838 views • link
updated by GenoMax GenoMax • written by a.rex a.rex

1 answer

Go to Flowcell_ID/Unaligned/Reports/html directory (or use the directory where you wrote the demux results/Reports/html) and view index.html using a browser.

• 0 views • link
written by GenoMax GenoMax

Thanks for this - I located the index.html but it is empty. However, the demultiplexed read fastqs have been made and are populated with reads....

• 0 views • link
written by a.rex a.rex

Sorry - my bad, I had to download the entire subset of html files to view the index.html as it made links to other I files (I presume).

• 0 views • link
written by a.rex a.rex

You could download a file called laneBarcode.html that is buried farther down in the Unaligned/Reports/html/barcode/all/all/all/ folder. That can be used standalone.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this