Question: Test data for bcl2fastq
0
gravatar for Christopher Bottoms
2.4 years ago by
Christopher Bottoms190 wrote:

Is there test data available for bcl2fastq? I found a script in the bcl2fastq distribution (i.e. src/bcl2fastq/data/generator/mkdata.sh) that generates bcl.bgzf files and a s_1.bci file (i.e. Lane BCI file, the "BCI Files" described in the bcl2fastq user guide), but I'm not sure how to create .bcl.bgzf.bci files (i.e. Cycle BCI files, which are not even mentioned in the user guide). I can't successfully run the latest version of bcl2fastq without these Cycle BCI files.

I'm specifically looking for a small dataset that will be processed quickly and hopefully with a license that I can redistribute.

sequencing bcl2fastq • 1.5k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Christopher Bottoms190
1
gravatar for h.mon
2.4 years ago by
h.mon29k
Brazil
h.mon29k wrote:

If you have a BaseSpace account:

1) log into it 2) Select "public data" at the top of the window - just after "apps" 3) Peruse the available datasets, some of them are available only as projects, some as runs, and some as both.

For example, an exome dataset available only as Run:

Run NovaSeq: TruSeq Exome (96 replicates of NA12878) (230 GB)
Project NovaSeq: TruSeq Exome (96 replicates of NA12878) ()

ADD COMMENTlink written 2.4 years ago by h.mon29k

Thanks! I haven't used BaseSpace, but perhaps I should look into a trial if the data is redistributable. Do they provide raw bcl data?

ADD REPLYlink written 2.4 years ago by Christopher Bottoms190

There is a free basic tier for BaseSpace, with 1Tb space. I think the runs include "raw" bcl data, as runs are converted into fastq by RTA orbcl2fastq.

ADD REPLYlink written 2.4 years ago by h.mon29k
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