Genboree Microbiome Toolset

Okay - finally over the first hurdle. Now I have real questions and two requests

1. Can I work on the project I have open or another while the microbiome sequences are loading and I am waiting on email confirmation?
2. Can I add in another file with additional metadata columns at this point ? Or do I have to start an entirely new database?

1. Can you make the input window larger? or zoomable or ?
2. will you add feature of being able to select multiple samples simultaneously? Can get very tedious very quickly with more than 10 samples - which is pretty common situation.

Thanks!!

Hello Toni-Ann,

Can I work on the project I have open or another while the microbiome sequences are loading and I am waiting on email confirmation?

• Yes, you can work on submitting jobs for multiple projects. In fact, you can submit two identical jobs as long as the folder names are different (by default we include a time stamp to avoid any repetitive folder names).

Can I add in another file with additional metadata columns at this point ? Or do I have to start an entirely new database?

• Yes, you can add a metadata file with additional metadata columns at this time. The samples that do not contain this metadata column will be filled in with 'noValue' to indicate that this appeared in one metadata set but not the other.

Can you make the input window larger? or zoomable or ?

• We will look into expanding the window area and potentially having a "zoomable" type of window which will allow you to see more than a handful of samples.

will you add feature of being able to select multiple samples simultaneously? Can get very tedious very quickly with more than 10 samples - which is pretty common situation.

• We are currently in the process of allowing the user to link samples with sequence files in bulk, which would be in place of the manual method.
• Currently, you can drag across the entire 'Samples' folder to the Output Targets window, which allows for sub-selecting of samples in the sequence importer step. This was once such example of how we were able to decrease the laborious task of dragging over of samples for one such process.

Thanks,
Kevin

Excellent!

I should have retried dragging the samples folder now that I got the green signal! Will do that next time for certain.

Will this work if I make sample sets ?

Hello Toni-Ann,
Yes. This will work for each time that you make a sample set. If you are making multiple sample sets I would recommend that you name them something informative like 'Sample_Set_A-samples1-20-Sequence-Import-2011-08-02-4:35:00', 'Sample_Set_B-samples21-40-Sequence-Import-2011-08-02-4:40:00', etc. You can then drag over the entire 'Samples' folder in which to perform the sequence import step instead of having to manually drag over each sample that has already been linked. Also, this step allows you to sub-select samples in the tool window in the case that you would like to select a sub-set of sequences, re-complete the sequence import but only remove a few samples, etc. This dramatically decreases the likelihood that a user will have to re-complete the uploading, sample import, and sample - file linker steps.
Thanks,
Kevin

I just tried this with a new 'db' and when I drag the entire sample folder over I get not green light to go ahead and link.

How can I view what I have in a sample set?

Hello Toni-Ann,
I'm glad you were able to get your experimental data through the pipeline!

How can I view what I have in a sample set?

We are currently testing the sample set utility set on the workbench. As soon as we have finished verifying the sample set functionality, we will be posting an updated tutorial illustrating our suggested usage of this new utility. We will keep you updated as to the progress of this task, but we should have something up within the next week or so.

Thanks!
Kevin

At which point in the QC screen is average read length calculated? Does the value reported in the sequence_metrics_summary file represent the average sequence length of: 1) all sequences that match their associated barcode, 2) all sequences that pass the QC filters, or 3) something else?

Thanks,
Emily

P.S. There are a couple of typos in the sequence_metrics_summary file headings. "sequence_length_shorter_then_min_after_trimming" and "sequence_qual_lower_then_min" should have "than" rather than "then".

Hello Emily,

Great question.

At which point in the QC screen is average read length calculated? Does the value reported in the sequence_metrics_summary file represent the average sequence length of: 1) all sequences that match their associated barcode, 2) all sequences that pass the QC filters, or 3) something else?

• The average read length is calculated based all sequences that pass the QC filters. Thus, the final sequence metrics (i.e. average read length) reflect the data that goes on to the various analysis pipelines.

We will also correct the spelling mistakes that you have identified.

Thanks for the feedback!
Kevin