"We've manage to get almost all plates downloaded with the FIMS data attached. There are some exceptions though. These exceptions seem to be due to a corrruption of the main FIMS excel file which is troubling. I've cut and pasted this…"
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Suzanne Nagi replied to Suzanne Nagi's discussion 'Query Taxon' in the group Biocode LIMS plugin"It appears to be very tempermental. I can download a pair of plates and have them all show their correct information and then an hour later download the same plate (withouth having edited it) and they will all read the generic answers i.e.…"
Suzanne Nagi replied to Suzanne Nagi's discussion 'Query Taxon' in the group Biocode LIMS plugin"The extraction, pcr, and sequence plates all show the correct genus, species etc. - its when I select "download traces from Lims" that the information seems to get lost."
Steven Stones-Havas replied to Suzanne Nagi's discussion 'Query Taxon' in the group Biocode LIMS plugin"Hi there Suzanne,
Are your reactions in the LIMS set up correctly (linked to the correct records in your FIMS database)? Search for one or more of your sequencing plates, and have a look at the wells (you can either double click on a well to…"
Suzanne Nagi added a discussion to the group Biocode LIMS plugin
Query Taxon
Hi. When I download traces from lims a large % of my sequences get assigned to the same (and mostly incorrect) genus - specifically "Sclerolobium sp. A PP" - in the organism column. Is there any way to change this either to reflect the actual species or genus or family of the samples or to select a broader default. We were looking forward to using the verify taxonomy function to check our results but with this issue its not much use. Thanks as always, SuzanneSee More
Steven Stones-Havas replied to Suzanne Nagi's discussion 'removing traces' in the group Biocode LIMS plugin"Unfortunately we don't currently have a way to do this, but I think it's an excellent idea for a feature. For the moment the only way to delete all traces on a plate is to either do them one by one, or to delete the entire plate and…"
Suzanne Nagi added a discussion to the group Biocode LIMS pluginremoving traces
Hi,Is there a way to bulk remove traces? I added my trace files to several plates twice and now have repeat sequence entries which are slowing down the analysis. Is there any way to efficiently get rid of these on a plate by plate basis?See More
Suzanne Nagi commented on Steven Stones-Havas's group 'Biocode LIMS plugin'"Hi,
Is there a way to bulk remove traces? I added my trace files to several plates twice and now have repeat sequence entries which are slowing down the analysis. Is there any way to efficiently get rid of these on a plate by plate basis?"
Steven Stones-Havas replied to Suzanne Nagi's discussion 'Trouble with Bulk Add Traces' in the group Biocode LIMS plugin"I think the problem is the .rbcl bit in the name is confusing the plugin. If you were searching for well numbers, Geneious is smart enough to realise that there is extra stuff added onto the end, but it's harder to do for arbitrary…"
Suzanne Nagi added a discussion to the group Biocode LIMS pluginTrouble with Bulk Add Traces
Hi! Whenever I try to import bulk traces I get the message "Imported 0 traces". I can add traces one by one which makes me think its a problem with the name matching. We are matching the GUID in the field data with the GUID in the ab1 file name. One problem that we are running into is that sometimes the GUID is the 3rd part of the name while other times it is the 4th, depending on how specifically the sample is classified. Also the next _ (seperator) is after a ".primer. Any suggestions on what…See More
Suzanne Nagi joined Steven Stones-Havas's groupBiocode LIMS plugin
The Biocode LIMS plugin is a free suite of plugins to Geneious that allow you to track and manage your entire lab workflow, from tissue samples through to Sequence analysis and Genbank Submission. Visit our website to download the plugins.See More
Profile Information
- Institution/Organization
- Smithsonian NHM
- Title/Position
- Other
- If Other Title, please specify
- Government contractor
- I’m involved in, or am interested in the following barcoding initiatives
- TreeBOL, DNA Barcoding Initiative for Conservation, Plant Working Group, Database Working Group, Data Analysis Working Group, Leading Labs Network
- I’m involved in or interested in the following iBOL Working Groups
- WG1.2 Land Plants, WG1.5 Agricultural and Forestry Pests and Their Parasitoids, WG1.7 Freshwater Bio-Surveillance, WG1.9 Terrestrial Bio-Surveillance, WG1.10 Polar Life, WG2.1 Barcoding Biotas, WG2.3 Methodological Innovation, WG2.4 Paleobarcoding, WG3.1 Core Functionality, WG4.1 Environmental Barcoding
- I’m involved in the following aspects of barcoding:
- Labwork/generating barcode sequences, Management of barcode data
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