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Hi again Steven,
We still are testing the Biocode plugin for the Sponge Barcoding Project and as general lab routine.
As we already accumulated quite some dozens of PCR and sequencing plates before using the Biocode plugin we are facing two problems for which me might need a feature modification:
1) It seems as if bulk assembly of forward and reverse sequences is not possible if the names of the sequences are too different (as it is for some of our older plates, in which forward and reverse sequence have different separators or orders). However, all the other metadata (sample ID, registration number etc), with which the correct forward and reverse sequences can clearly be identified, are displayed in the viewer, but they cannot be chosen in the "Data" filed of the Assembly popup-window. Would there be a chance to include a way that corresponding sequences are likewise recognized by other data fields than only the sequence names?
2) I might have not found this feature, but is there a way to upload older cherry picking plates (i.e. not generated by the plugin, but by ourselves), and how will this data be linked to the FIMS?
Thanks a lot and best regards,
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.
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?
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,
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.
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,
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.
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,
We are currently facing exactly the same problem. Is there any solution around?