Dealing with old barcoding data

Replies to This Discussion

Permalink Reply by Steven Stones-Havas on February 20, 2011 at 5:15pm

Thanks, Dirk,  Your feedback is always appreciated.

 

1)  It sounds to me like the best solution would be to use our batch rename feature on your reads before you assemble them (you can find it in the edit menu).  You can choose to rename your sequences with any combination of your data fields, and they should then assemble fine.

 

2) There are a couple of ways you can do this:

 

* If you are creating a cherry-picked extraction plate, and you are using 2D barcodes, you can paste the ist of barcodes into the plate bulk-editor, then click "Fetch extractions from barcodes" in the tools menu.

 

*You can paste tissue and extraction ids into the bulk editor, and when you save the plate, it will move those extraction records to your new plate.

 

Permalink Reply by Jonas Astrin on February 23, 2011 at 3:37am

I've got a question relating to 'old barcoding data' as well, so I append it here, although it is related to those data generated with Biocode using a local DB:

once we switch to an external SQL database to hold the LIMS data (instead of locally within Geneious), is there a 'sophisticated' way to transfer the data, which seem to consist of a number of XML files, from Geneious to this DB?

Thanks

  Jonas

Permalink Reply by Dirk Erpenbeck on June 25, 2012 at 4:19pm

Hi Steve,

Cool, we finally got to this problem and it works. I like the "bulk editor" function for our folders of .abi traces, however, do I see it correctly that when I want to use "Bulk add traces" for cycle sequencing reactions, I can only select a folder on my desktop (or anywhere else on my computer) instead of directly selecting my bulk-renamed-.abi files in Geneious? Do I always have to do the detour with exporting the renamed files on my desktop before re-importing into the Biocode?

Thanks for your suggestion and cheers,

Dirk

Permalink Reply by Steven Stones-Havas on June 25, 2012 at 6:42pm

Hi Dirk,

Our recommended protocol is to bulk load your traces onto the plates first, then download them from the plates into Geneious as that makes sure that the traces are correctly annotated with the LIMS and FIMS information.  You can do it the other way around, however.  If your traces are correctly annotated with FIMS and LIMS data in Geneious, then when you mark them as passed or failed, check the checkbox that says "also add my traces", and your traces will be attached to the correct plates.

cheers

Steve

Permalink Reply by Dirk Erpenbeck on June 27, 2012 at 1:05pm

Hi Steve,

Thanks for your quick answer again!

Here's a new question again (you see we are VERY busy with your program) for which you might have a logic answer:

When I assemble sequences and would like to upload them to the LIMS as "pass" or "fail" after the verify taxonomy step, I highlight the assembly and use the appropriate "mark as... in LIMS" button (as suggested in the video). The subsequent window reminds me that the consensus is saved as well (which is great, as this is what we want), and allows me to save the traces as well (what I do).

Anyway, when I search for the sequences in Biocode again (all search options ticked) after uploading, I obtain two nucleotide documents called "<extractionID> <locus>" and both described as "Assembly consensus sequence for <extractionID> <locus>". However sequences are just the nucleotides of the forward and reverse traces in separate files (so not the consensus at all, see the screenshot). 

I would expect after the search:

1) one single nucleotide document with the consensus of the assembly

2) the forward and reverse trace files appearing.

Any idea where I can find the files?

Thanks so much again and cheers,

Dirk

Permalink Reply by Steven Stones-Havas on June 28, 2012 at 2:57am

Hi Dirk,

Marking an assembly as passed should result in a single sequence (the consensus sequence of that assembly).  The traces never appear in the search results directly - they appear in the plates themselves (double click on a well and select "add/edit traces" to see).

The only thing I can think of is that your workflow of annotating the traces first and then adding the traces to the plates is somehow exposing a bug in the plugin.  I'll look into it - we're hoping to put a patch release in the next week or two with a bunch of fixes, so if this turns out to be a problem it will be included in that release.

cheers

Steve

Permalink Reply by Dirk Erpenbeck on August 2, 2012 at 9:28am

Hi Steve,

back on this issue -

First thanks for the information, but the problem remains. I tried several approaches (annotatad traces, raw traces etc and followed your suggestion and the workflow shown in the video-tutorial). When I  use "Mark as pass in LIMS" on an assembly and try to retrieve the consensus afterwards from the LIMS I still get the forward and reverse sequence (as 2 different nucleotide documents both titled by with the extraction ID) but not the consensus ( I use same consensus options as in the tutorial, I currently use Geneious 5.6.5. and Biocode 2.3.3).

Any fix for this in the coming patch maybe?

Thanks and cheers,

Dirk

Permalink Reply by Guy Colling on September 5, 2012 at 9:35am

Dear Steve,

We are currently facing exactly the same problem. Is there any solution around?

Best wishes,

Guy