http://www.progenygenetics.com/community/ Progeny Community » Forum: Progeny Lab - Recent Posts en Sun, 05 Feb 2012 16:54:16 +0000 http://www.progenygenetics.com/community/topic/175#post-576 Tue, 18 Oct 2011 14:10:39 +0000 Conrad Brammer 576@http://www.progenygenetics.com/community/ <p>Thanks for the suggestion, Jesse. </p> <p>It seems like this would be a very helpful feature for quite a few of our users. I have logged this into our system with a ticket ID of C1463. Our next review is scheduled for this Friday, the 21st, and this issue has already been submitted. We will notify you here when this issue has been addressed by our development department. </p> <p>Thanks for the post! </p> http://www.progenygenetics.com/community/topic/175#post-572 Mon, 17 Oct 2011 12:36:26 +0000 mccanejd 572@http://www.progenygenetics.com/community/ <p>Hello,</p> <p>I've noticed that dragging and dropping samples onto a plate while in the plate viewer module only allows loading of samples onto the plate by row (across). In our lab protocols, we build our plates by column (i.e. sample 1 in A1, sample 2 in B1, sample 3 in C1...sample 9 in A2, sample 10 in B2, etc.). It would be very useful for us if there was an option in Progeny to toggle the loading of samples onto a plate by column or by row when using the drag and drop method. This function would save us a lot of time over importing a .txt file. Any chance we could see this feature in a future Progeny update?</p> <p>Thanks!</p> <p>-Jesse </p> http://www.progenygenetics.com/community/topic/137#post-531 Tue, 09 Aug 2011 09:44:42 +0000 jennifer-rigdon 531@http://www.progenygenetics.com/community/ <p>Wonderful news! Thanks! </p> http://www.progenygenetics.com/community/topic/137#post-514 Mon, 25 Jul 2011 19:42:21 +0000 Conrad Brammer 514@http://www.progenygenetics.com/community/ <p>Hi Jennifer, </p> <p>Just wanted to let you know that your request to have custom exports zero out the founders parents (tracking ID - C1273) has been coded into the software and will be included in our next release. The next release is currently scheduled for the week of August the 8th. </p> <p>As always, a big thanks to you and the rest of the Progeny community for sharing your ideas and suggestions to make our software a more useful tool! </p> http://www.progenygenetics.com/community/topic/137#post-467 Wed, 01 Jun 2011 18:10:19 +0000 Conrad Brammer 467@http://www.progenygenetics.com/community/ <p>This is a feature that is new to Progeny 8. </p> <p>Much of this is detailed in our user manual, so we will first get you a copy of that. If you still have questions after reading the manual please let us know. </p> <p>Genotypes that are stored at the sample level can be exported as individual level fields if they are set as the 'Primary Sample' for that individual. Outside of this use, this data cannot be viewed or exported as individual fields. </p> <p>Hope this helps! </p> http://www.progenygenetics.com/community/topic/137#post-462 Wed, 01 Jun 2011 10:28:32 +0000 Toby McHenry 462@http://www.progenygenetics.com/community/ <p>Is the ability to import genotypes at the sample level versus the individual level something Progeny 7 can do, or is this something new with Progeny 8? </p> <p>I didn't know multiple genotypes could be stored for a single person, so I'm interested to learn more about this. If there is further documentation on this, could you direct me there? Are genotypes imported at the sample level viewable and/or exportable as individual fields? I would like to know more.</p> <p>Thanks!! </p> http://www.progenygenetics.com/community/topic/137#post-445 Tue, 10 May 2011 15:58:57 +0000 Conrad Brammer 445@http://www.progenygenetics.com/community/ <p>Thanks for the suggestion, Jennifer. </p> <p>I've logged your request as well, and your tracking ID for this request is C1273. </p> http://www.progenygenetics.com/community/topic/137#post-430 Wed, 04 May 2011 11:11:45 +0000 jennifer-rigdon 430@http://www.progenygenetics.com/community/ <p>For a lab feature to consider... having the custom export zero the founders parents :) just thought I would re-add my thought since you offered!<br /> Thanks! </p> http://www.progenygenetics.com/community/topic/137#post-429 Tue, 03 May 2011 17:56:16 +0000 Conrad Brammer 429@http://www.progenygenetics.com/community/ <p>Hello Jesse, </p> <p>Have you imported genotypes for those individuals at any point in time before you imported the genotypes for ethanol and blotter samples? </p> <p>The reason I ask is because any genotype values that had previously been stored at the "Individual Level" would not have been updated when you ran your last import. Since you imported into the "Sample Level" only, this would update genotype values for the samples while leaving all "Individual Level" genotypes intact.</p> <p>For example, if you ran a genotype import "GenoRun_A" into both the Sample AND Individual Levels, then Individual_1, Sample_1 and Sample_2 would all have genotypes from "GenoRun_A" </p> <p>Now, if you run a genotype import "GenoRun_B" into ONLY the Sample Level, then Sample_1 and Sample_2 would then have genotypes for "GenoRun_B" but Individual_1 would still have genotypes for "GenoRun_A".</p> <p>This situation might explain why you saw values for "Individual" that did not match either sample from your genotype import. If you want to clear all genotypes that are currently stored at the Individual Level you should clear the genotypes for your individuals and retain the genotypes for only the samples. You can do this by clicking the "Clear Genotyping" button from the toolbar and clearing the genotypes for your individuals. </p> <p>We will be spending several development cycles here in about 2 - 3 months that will be devoted entirely to improving Lab features. If there are any features like this that you would like us to improve upon, please let us know what you would like to see before then and I'll make sure your requests are logged into our system and addressed.</p> <p>Thanks, </p> <p>Conrad </p> http://www.progenygenetics.com/community/topic/137#post-428 Tue, 03 May 2011 12:43:20 +0000 mccanejd 428@http://www.progenygenetics.com/community/ <p>I think I may have figured out what my problem was. It turns out that neither the blotter paper sample nor the ethanol sample were selected as the primary sample for these individuals. Instead, when I right click on one of the individuals and go to "Choose Primary Sample", "Individual" was selected rather than the ethanol sample or the blotter sample. So I went through and selected the ethanol sample as the primary sample for each of the individuals, re-ran the export, and the genotypes now look much better. So it seems that when "Individual" was selected as the primary sample, it was exporting some strange mix of the two sample genotypes, even though no genotype was stored for these individuals on the individual level. It might be worth fixing this to where if you export individuals who have multiple genotypes at the sample level and where "Individual" is selected as the primary sample, blank data gets exported rather than the strange results I was seeing before. </p> http://www.progenygenetics.com/community/topic/137#post-427 Tue, 03 May 2011 12:28:30 +0000 mccanejd 427@http://www.progenygenetics.com/community/ <p>Hello,</p> <p>I've run into something strange when doing a custom export for individuals who have two different genotypes stored at the sample level. Here's a little background: recently we received a set of samples, in which there were two samples for each individual. The purpose of this study was to examine two different sample preservation methods - ethanol versus blotter paper. So I created the individuals in Progeny, and created two samples for each individual. I then imported the genotypes on the sample level. So at this point each individual had two samples, each with it's own imported genotype. However, when I ran an export of the individuals, the genotypes came out pretty wacky...in some cases the allele A and B were switched, in other cases one allele was a no call and the other an A/C/G/T, and for a few fish the exported allele A/B didn't match the genotypes for either of the samples from the raw import data. I was under the assumption that when you export genotype data for an individual that has multiple samples with their own genotypes, it would export the genotype for the individual's primary sample...any idea what might be going on here?</p> <p>Thanks,</p> <p>-Jesse </p> http://www.progenygenetics.com/community/topic/129#post-404 Thu, 14 Apr 2011 10:06:09 +0000 jennifer-rigdon 404@http://www.progenygenetics.com/community/ <p>Thanks, what would be really helpful! </p> http://www.progenygenetics.com/community/topic/129#post-403 Thu, 14 Apr 2011 09:29:43 +0000 Michael Brammer 403@http://www.progenygenetics.com/community/ <p>Jennifer,</p> <p>Currently, the Custom Export option does not allow you to zero out the parent id's of the founders. We'll add this to the list and see if we can release it in an forthcoming update. </p> http://www.progenygenetics.com/community/topic/129#post-386 Tue, 12 Apr 2011 10:46:51 +0000 jennifer-rigdon 386@http://www.progenygenetics.com/community/ <p>We often export genotypes from just a cropped portion of our pedigrees. When this is done using the FBAT option, the founders mother ID and father ID are zeroed (even if they exist in the pedigree). When this is done using the Custom option, the founders parents are not zeroed and their IDs are included, even if they are not a part of the cropped pedigree that is being exported. I was wondering about the possibility of the custom option zeroing the parent IDs of the founders. I was hoping that since this is possible via the FBAT option, it could be possible via the custom option? Any ideas you have regarding this would be nice. Thanks. </p> http://www.progenygenetics.com/community/topic/34#post-341 Fri, 01 Apr 2011 18:44:33 +0000 David DeRam 341@http://www.progenygenetics.com/community/ <p>Yes. This feature is now available in version 8.1.</p> <p>Very much appreciate the suggestion. </p> http://www.progenygenetics.com/community/topic/103#post-339 Fri, 01 Apr 2011 18:36:41 +0000 David DeRam 339@http://www.progenygenetics.com/community/ <p>We are in a stage where we just need to get the specifics. We've done this for SNPs with Ensembl, dbSNP, UCSC, etc. It's a similar process. If you can provide us the details we are happy to implement those connections. Otherwise we can pull them from the documentation. After we have the details the implementation will be speedy. </p> http://www.progenygenetics.com/community/topic/34#post-338 Fri, 01 Apr 2011 13:27:00 +0000 Ginny Hughes 338@http://www.progenygenetics.com/community/ <p>is this in version 8.1? </p> http://www.progenygenetics.com/community/topic/103#post-336 Fri, 01 Apr 2011 13:21:04 +0000 Ginny Hughes 336@http://www.progenygenetics.com/community/ <p>any update on this? thanks! </p> http://www.progenygenetics.com/community/topic/78#post-304 Tue, 01 Mar 2011 19:09:43 +0000 Conrad Brammer 304@http://www.progenygenetics.com/community/ <p>It is necessary in Progeny that you import your markers into a set, but if you wanted to update all of your markers, you can import a super set that uses all of your markers. Thus you would be able to update "All Markers" with one import, and simply delete the set. </p> <p>This should serve as an effective method for updating "All Markers".</p> <p>Thanks for the post! </p> http://www.progenygenetics.com/community/topic/78#post-303 Tue, 01 Mar 2011 11:58:55 +0000 Toby McHenry 303@http://www.progenygenetics.com/community/ <p>Do I have to do this for each marker set individually, or is there a way to do this once for all markers?</p> <p>Thanks! </p> http://www.progenygenetics.com/community/topic/111#post-292 Tue, 15 Feb 2011 17:44:21 +0000 jamie-lheureux 292@http://www.progenygenetics.com/community/ <p>We use UCSC genome browser: <a href="http://genome.ucsc.edu/cgi-bin/hgGateway" rel="nofollow">http://genome.ucsc.edu/cgi-bin/hgGateway</a> </p> http://www.progenygenetics.com/community/topic/111#post-286 Mon, 14 Feb 2011 18:46:00 +0000 Conrad Brammer 286@http://www.progenygenetics.com/community/ <p>The base pairs should be provided to you along with your marker sets. What ever source you use for your marker sets should be the same source you use to retrieve those values.</p> <p>Thanks for the post! </p> http://www.progenygenetics.com/community/topic/111#post-283 Fri, 11 Feb 2011 16:31:20 +0000 LabRat 283@http://www.progenygenetics.com/community/ <p>In Progeny Lab, under markers, a required field is "base pairs" which is described in the user manual as "Total number base pairs from beginning of chromosome." In our lab, we refer to the position of the SNP by referencing the arm of the chromosome (for example 4q31.2 for the SNP EDNRA3, AKA rs6537484). I am wondering if there is some web resouce where I could use this information to find what the software is asking for. Any suggestions? </p> http://www.progenygenetics.com/community/topic/103#post-266 Fri, 21 Jan 2011 11:34:11 +0000 David DeRam 266@http://www.progenygenetics.com/community/ <p>Yes we can provide this functionality and we have already discussed internally. We need to get details on the specific parameters for each database. This has been entered into our system. We will contact you when the feature is available or if we have questions.</p> <p>Thank you! </p> http://www.progenygenetics.com/community/topic/103#post-264 Thu, 20 Jan 2011 10:23:03 +0000 Ginny Hughes 264@http://www.progenygenetics.com/community/ <p>Does Progeny have a plan to be able to connect (via the marker module) to public CNV databases (Database of genomic variants = <a href="http://projects.tcag.ca/variation/" rel="nofollow">http://projects.tcag.ca/variation/</a>; 2. DECIPHER database = <a href="https://decipher.sanger.ac.uk/" rel="nofollow">https://decipher.sanger.ac.uk/</a><br /> 3. ECARUCA = <a href="http://agserver01.azn.nl:8080/ecaruca/ecaruca.jsp" rel="nofollow">http://agserver01.azn.nl:8080/ecaruca/ecaruca.jsp</a>; 4 dbvar.</p> <p>thanks </p> http://www.progenygenetics.com/community/topic/96#post-243 Wed, 05 Jan 2011 19:06:51 +0000 jamie-lheureux 243@http://www.progenygenetics.com/community/ <p>Thanks for the response. The strange thing is that we always create our plates in the plate section. We don't want to have them in the freezer section at all, but about 25% of the time they also end up in the freezer section and we don't know why. Last week, one person created 13 plates all in the plate section, right in a row, in the exact same way (as far as we can tell) and 3 of them showed up in the freezer section. That is what prompted the question. I guess we will just ignore them in the freezer section for now and when we switch to 8 they will all be in there. </p> http://www.progenygenetics.com/community/topic/96#post-240 Mon, 03 Jan 2011 16:37:11 +0000 Conrad Brammer 240@http://www.progenygenetics.com/community/ <p>In Progeny 7, if a plate gets created in the Plates section, it will not show up in the Freezers section. </p> <p>Any plate that gets created in the Freezers section, however, will always be added to the “Added Plates” folder of the Plates section. The only way to get a plate added to the Freezers section is to create the plate in the Freezers section. So, for the time being, any plates that have already been created in the Plates section cannot be "moved" into the Freezers section.</p> <p>The conversion to Progeny 8 will account for this. All plates that exist in Plates but are not accounted for in Freezers get added to Freezers at the root level when you run your database maintenance. It would be possible for you to update these plates manually, though it is somewhat of an involved process. Since the release of Progeny 8 is right around the corner, it might make sense to hold off until you can run the update. I'll give you a step-by-step and you can make the call. Here is how I would recommend updating those plates manually:</p> <p>1. Run a sample spreadsheet over all of the samples that are in a container that does not exist in Freezers with 3 columns (Sample Name, Container Name, Position) and export that spreadsheet.<br /> 2. Delete all the plates from the Plates module that do not exist in Freezers and recreate those plates in Freezers one-by-one<br /> 3. Lastly, reimport the data you just exported in step #1 via the Import Module using the respective 3 columns: Sample Name, Container Name and Position. </p> <p>This will leave you will all of you plates in both locations. To avoid this problem before converting to Progeny 8, simply create your plates in the Freezer section. That way they will be represented in both locations.</p> <p>Thanks for the post!</p> <p>Conrad </p> http://www.progenygenetics.com/community/topic/96#post-238 Wed, 29 Dec 2010 17:35:41 +0000 jamie-lheureux 238@http://www.progenygenetics.com/community/ <p>When we create new plates in the plate section and import samples into them, sometimes they also show up in the freezer section, but sometimes they do not. We can't seem to figure out what it is that determines whether they will also appear in freezers. Is there something we are accidentally doing differently from plate to plate? Thanks!<br /> Jamie </p> http://www.progenygenetics.com/community/topic/94#post-235 Sat, 18 Dec 2010 15:25:20 +0000 David DeRam 235@http://www.progenygenetics.com/community/ <p>Yes! There is a way to do this without having to reenter the aliquots.</p> <p>You can use the import module to add new aliquots to existing parent samples...but you can also use the "Update Sample if found" option in the import module to update existing aliquots.</p> <p>This is what you will do in your scenario. You will turn on the "Update Sample if found" option and include the "Parent Sample Name" as an import column. The result will be that your current aliquots will be tied to the parent samples that you recreated.</p> <p>To get to the samples import module start from the Samples navigation tab and click "Import" on the toolbar. Your import can simply be 2 columns:<br /> 1. Sample Name (the sample name of the aliquot)<br /> 2. Parent Sample Name (the sample name of the parent sample)</p> <p>The file you import will look something like this. (Aliquots1-5 will be tied to Parents 1-3).</p> <p>ALIQUOT1, PARENT1<br /> ALIQUOT2, PARENT2<br /> ALIQUOT3, PARENT3<br /> ALIQUOT4, PARENT3<br /> ALIQUOT5, PARENT3 </p> http://www.progenygenetics.com/community/topic/94#post-234 Fri, 17 Dec 2010 13:09:36 +0000 larae019 234@http://www.progenygenetics.com/community/ <p>On accident, I managed to delete several parent samples from the database. The aliquots for these samples were not deleted. After recreating the parent samples, I can't figure out how to add the existing aliquots to this new parent sample. Is there a way to do it without having to reenter the aliquots? Thank you. </p>