Question: How do I access statistics for read counts after demultiplexing in bcl2fastq?
0
gravatar for a.rex
10 days ago by
a.rex60
a.rex60 wrote:

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 • 177 views
ADD COMMENTlink modified 10 days ago by genomax32k • written 10 days ago by a.rex60
2
gravatar for genomax
10 days ago by
genomax32k
United States
genomax32k wrote:

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.

ADD COMMENTlink modified 10 days ago • written 10 days ago by genomax32k

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....

ADD REPLYlink modified 10 days ago • written 10 days ago by a.rex60

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).

ADD REPLYlink written 10 days ago by a.rex60
1

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.

ADD REPLYlink modified 10 days ago • written 10 days ago by genomax32k
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