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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, Suzanne
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Replies to This Discussion
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Permalink Reply by Steven Stones-Havas on -
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 open it, or change the display options to show genus on the plate view itself). I suspect the problem might be that your extraction reactions are not connected to the right tissue records, and as taxonomy propagates from there through all workflows in the LIMS, the mistake would be carried through all the way to the traces.
If this is the case, then to fix the problem you would need to go back to the extraction plates, and edit their tissue id's to point to the correct tissue records (there are bulk editing tools to do this in the plate viewer)
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Permalink Reply by Suzanne Nagi on -
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.
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Permalink Reply by Suzanne Nagi on
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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. Sclerolobium sp. A PP. And vice versa. Maybe it has something to do with how many other processes are running in the program?
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Permalink Reply by Suzanne Nagi on
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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 trouble plate data into a new spreadsheet and by recreating plates have everything run fine. However, when I run the data back in our original FIMS excel file the data does not transfer during the "download traces from LIMS" process.
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