Question: How do I access statistics for read counts after demultiplexing in bcl2fastq?
0
gravatar for a.rex
9 weeks ago by
a.rex80
a.rex80 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 • 229 views
ADD COMMENTlink modified 9 weeks ago by genomax34k • written 9 weeks ago by a.rex80
2
gravatar for genomax
9 weeks ago by
genomax34k
United States
genomax34k 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 9 weeks ago • written 9 weeks ago by genomax34k

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 9 weeks ago • written 9 weeks ago by a.rex80

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 9 weeks ago by a.rex80
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 9 weeks ago • written 9 weeks ago by genomax34k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 793 users visited in the last hour