http://www.progenygenetics.com/community/ Progeny Community » Forum: Progeny Lab - Recent Topics en Sun, 05 Feb 2012 17:51:06 +0000 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-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-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-50 Thu, 15 Jan 2009 14:19:03 +0000 Ginny Hughes 50@http://www.progenygenetics.com/community/ <p>It would be most helpful to be able to query on pedigree fields (i.e we might want to pull out only pedigrees that have a familial mode of inheritance). IS there a way to do this? </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/78#post-166 Wed, 01 Sep 2010 14:02:48 +0000 Toby McHenry 166@http://www.progenygenetics.com/community/ <p>If I want to change the bp position of all my markers (for example, to upgrade from the 2004 build positions to the 2006 positions), do I need to use the SQL backend to do this? Or is there a front end way to make this change? </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/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-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> http://www.progenygenetics.com/community/topic/77#post-165 Wed, 01 Sep 2010 14:01:28 +0000 Toby McHenry 165@http://www.progenygenetics.com/community/ <p>I had a question about doing a genotype import when there are a large number of discrepancies. Is there a way to tell Progeny to select A1new and A2new for all markers in the discrepancy tab rather then have to click them all by hand? </p> http://www.progenygenetics.com/community/topic/74#post-159 Tue, 20 Jul 2010 11:57:40 +0000 ldowns 159@http://www.progenygenetics.com/community/ <p>I have a marker set of over 180 000 SNPs, but am struggling to get hold of the standard alleles for the set. </p> <p>I am under the impression (from the user manual) that the standard alleles are optional, and therefore not required, but when I try to import the genotyping data it all gets rejected with the message "Invalid SNP (no allele match for ACTG)".<br /> I am certain it has to do with the standard alleles, because I have worked them out from the genotyping data for a couple of markers, and when the markers have standard alleles defined, the genotype imports work perfectly.</p> <p>Please can someone help me with this?</p> <p>Thank you </p> http://www.progenygenetics.com/community/topic/62#post-121 Mon, 02 Nov 2009 18:20:37 +0000 jamie-lheureux 121@http://www.progenygenetics.com/community/ <p>We have a few markers that are in all markers that we can't get to add to sets. I have tried adding it to the set by right clicking on the set and selecting 'add markers to this set'. It seems like it gets added (and the others that were with it are added) but when we try to import into the set or search the set it can't be found. Are there any restrictions on marker names or perhaps the alias for markers in marker sets? The names seem particularly long, so I am wondering if there is a restriction on the number of characters? Thanks! </p> http://www.progenygenetics.com/community/topic/40#post-65 Fri, 06 Feb 2009 12:51:00 +0000 Ginny Hughes 65@http://www.progenygenetics.com/community/ <p>Within the analysis module, it would be helpful to have an option to include only people on a particular plate in the analysis. Currently when you pull a plate into the "pedigree" box, it is not just the people on the plate that are included in the query, but everyone in the pedigree. Currently there is no way of selecting just the people on the plate for analysis. </p> http://www.progenygenetics.com/community/topic/30#post-45 Thu, 11 Dec 2008 10:32:28 +0000 Lizr 45@http://www.progenygenetics.com/community/ <p>I find the discrepency checks very useful for checking our data generated on the genome wide platform with our taqman genertaed data for validating SNP's. It is very useful to see if we have a platform issue when validating these SNP's. However Currently the database registers AB and BA as discrepent - which they aren't. This is really frustrating when you have to go through 1000's of these. I really only want to know if an genotype goes from for example AB to BB or AA, or if there is typing but the second assay is null. Currently we are working on 7.5.0.</p> <p>Can you let me know if the latest version does correct this problem? </p>