https://sourceforge.net/p/simulates/activity/Recent activity for SimulaTEenWed, 24 Feb 2021 10:18:50 -0000https://sourceforge.net/p/simulates/code/88/updated flo-helperRobert KoflerWed, 24 Feb 2021 10:18:50 -0000https://sourceforge.net/p/simulates/code/88/https://sourceforge.net/p/simulates/code/87/for flo added roRobert KoflerTue, 26 Jan 2021 13:55:59 -0000https://sourceforge.net/p/simulates/code/87/https://sourceforge.net/p/simulates/discussion/general/thread/2720a955ce/?limit=50#8750Hi Solomon, sorry for the late response, I only found your comment just now. You can provide a pgd-file that mirrors the proportion of TEs in the human genome. But this pgd file needs to be generated manually. You can not just enter proportions, you need to specify the insertion sites of each TE. But you could write a script that translates the proportions into a pgd files with random insertions sites for example. cheers roRobert KoflerFri, 24 Jan 2020 10:26:09 -0000https://sourceforge.net/p/simulates/discussion/general/thread/2720a955ce/?limit=50#8750https://sourceforge.net/p/simulates/discussion/general/thread/2720a955ce/?limit=25#8ed2Hi, I want to simulate genomes with different proportions of TEs, say, based on the human genome. Will SimulaTE be able to do that?Solomon ChakThu, 19 Sep 2019 01:40:17 -0000https://sourceforge.net/p/simulates/discussion/general/thread/2720a955ce/?limit=25#8ed2https://sourceforge.net/p/simulates/discussion/general/thread/e214d7f048/?limit=25#285cHi, I want to simulate genomes with different proportions of TEs, say, based on the human genome. Will SimulaTE be able to do that?Solomon ChakThu, 19 Sep 2019 01:39:51 -0000https://sourceforge.net/p/simulates/discussion/general/thread/e214d7f048/?limit=25#285chttps://sourceforge.net/p/simulates/discussion/general/thread/9f4e78b827/?limit=50#d816Hi Roxane, unfortunatelly SimulaTE does not support multiple chromosomes. Mostly because i did not think it is necessary when simulating TE landscapes. Simulated landscapes are mostly used for evaluating different tools where chromosomes are usually not important. So my first question would be: are you absolutly sure you need multiple chromsomes? In case you absolutely do need them the only way I can think of is concatenating the sequences of your chromosomes and maybe enter a easily recognizable...Robert KoflerTue, 26 Feb 2019 21:04:51 -0000https://sourceforge.net/p/simulates/discussion/general/thread/9f4e78b827/?limit=50#d816https://sourceforge.net/p/simulates/discussion/general/thread/9f4e78b827/?limit=25#e46bHi, Does SimulaTE recognise chromosome positions in the pgd file? E.g: Chasis hs37d5; Length 2867688499 nt 1=$1 # L19088.1 Human LINE1 (L1.3) repetitive element DNA sequence chr1:1327571 1- chr2:3743706 1+ chr3:17103970 * * If not, how could one go about creating a pdg file for a whole genome containing multiple chromosomes? Kindest regards, Roxane Roxane DunbarSun, 24 Feb 2019 21:36:24 -0000https://sourceforge.net/p/simulates/discussion/general/thread/9f4e78b827/?limit=25#e46bhttps://sourceforge.net/p/simulates/wiki/describing_TE_sequences/describing_TE_sequencesRobert KoflerThu, 18 Oct 2018 11:59:15 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/https://sourceforge.net/p/simulates/code/86/cleanupRobert KoflerMon, 16 Apr 2018 15:36:57 -0000https://sourceforge.net/p/simulates/code/86/https://sourceforge.net/p/simulates/code/85/enhanced reverse complementing, thanks to LukasRobert KoflerFri, 06 Apr 2018 10:06:04 -0000https://sourceforge.net/p/simulates/code/85/https://sourceforge.net/p/simulates/code/84/bug fix thanks to LukasRobert KoflerWed, 07 Mar 2018 14:52:17 -0000https://sourceforge.net/p/simulates/code/84/https://sourceforge.net/p/simulates/code/83/updated pacbio fasta writer; header contains also the read lengthRobert KoflerTue, 20 Feb 2018 12:33:21 -0000https://sourceforge.net/p/simulates/code/83/https://sourceforge.net/p/simulates/code/82/updated pacbio fasta writer; header contains also the read lengthRobert KoflerTue, 20 Feb 2018 12:32:28 -0000https://sourceforge.net/p/simulates/code/82/https://sourceforge.net/p/simulates/wiki/Walkthrough/WalkthroughRobert KoflerMon, 11 Dec 2017 10:42:38 -0000https://sourceforge.net/p/simulates/wiki/Walkthrough/https://sourceforge.net/p/simulates/wiki/Walkthrough/WalkthroughRobert KoflerMon, 11 Dec 2017 10:39:51 -0000https://sourceforge.net/p/simulates/wiki/Walkthrough/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerMon, 27 Nov 2017 10:49:16 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/special_use_cases/special_use_casesRobert KoflerMon, 16 Oct 2017 13:09:50 -0000https://sourceforge.net/p/simulates/wiki/special_use_cases/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 09 Oct 2017 14:20:33 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 09 Oct 2017 14:18:54 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 09 Oct 2017 14:16:43 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/special_use_cases/special_use_casesRobert KoflerMon, 09 Oct 2017 13:48:10 -0000https://sourceforge.net/p/simulates/wiki/special_use_cases/https://sourceforge.net/p/simulates/wiki/special_use_cases/special_use_casesRobert KoflerMon, 09 Oct 2017 13:31:15 -0000https://sourceforge.net/p/simulates/wiki/special_use_cases/https://sourceforge.net/p/simulates/wiki/special_use_cases/special_use_casesRobert KoflerMon, 09 Oct 2017 13:30:39 -0000https://sourceforge.net/p/simulates/wiki/special_use_cases/https://sourceforge.net/p/simulates/wiki/special_use_cases/special_use_casesRobert KoflerMon, 09 Oct 2017 13:29:56 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2017 09:46:53 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 09 Oct 2017 09:44:21 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 09 Oct 2017 09:41:19 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerMon, 09 Oct 2017 09:30:56 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerMon, 09 Oct 2017 09:30:44 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 09 Oct 2017 09:28:55 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 09 Oct 2017 09:22:27 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.nethttps%3A//sourceforge.net/projects/simulates/files/releases/simulate_v1.13.zip/downloadSimulaTEMon, 09 Oct 2017 08:58:03 -0000https://sourceforge.net/projects/simulates/files/releases/simulate_v1.13.zip/downloadhttps://sourceforge.net/p/simulates/wiki/Validation_Pop2/Validation_Pop2Robert KoflerMon, 09 Oct 2017 08:42:36 -0000https://sourceforge.net/p/simulates/wiki/Validation_Pop2/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerMon, 09 Oct 2017 08:40:43 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.nethttps%3A//sourceforge.net/projects/simulates/files/validation_pop2/tehier-ml100noS4.txt/downloadSimulaTEMon, 09 Oct 2017 08:40:01 -0000https://sourceforge.net/projects/simulates/files/validation_pop2/tehier-ml100noS4.txt/downloadhttps://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/TheClassic_SanMiguel_TELandscapeRobert KoflerSun, 13 Aug 2017 05:02:24 -0000https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/TheClassic_SanMiguel_TELandscapeRobert KoflerFri, 28 Jul 2017 13:25:37 -0000https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerFri, 28 Jul 2017 13:22:37 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerFri, 28 Jul 2017 13:22:01 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/Validate_unit_tests/Validate_unit_testsRobert KoflerTue, 25 Jul 2017 13:43:01 -0000https://sourceforge.net/p/simulates/wiki/Validate_unit_tests/https://sourceforge.net/p/simulates/wiki/Validate_reads/Validate_readsRobert KoflerTue, 25 Jul 2017 13:40:28 -0000https://sourceforge.net/p/simulates/wiki/Validate_reads/https://sourceforge.net/p/simulates/wiki/Validate_reads/Validate_readsRobert KoflerTue, 25 Jul 2017 13:33:37 -0000https://sourceforge.net/p/simulates/wiki/Validate_reads/https://sourceforge.net/p/simulates/wiki/Validation_Pop2/Validation_Pop2Robert KoflerTue, 25 Jul 2017 13:22:40 -0000https://sourceforge.net/p/simulates/wiki/Validation_Pop2/https://sourceforge.net/p/simulates/wiki/Walkthrough_toy/Walkthrough_toyRobert KoflerTue, 25 Jul 2017 13:09:15 -0000https://sourceforge.net/p/simulates/wiki/Walkthrough_toy/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerTue, 25 Jul 2017 13:03:59 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerTue, 25 Jul 2017 13:02:48 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/Walkthrough_species_tool_compatibility/Walkthrough_species_tool_compatibilityRobert KoflerTue, 25 Jul 2017 13:02:19 -0000https://sourceforge.net/p/simulates/wiki/Walkthrough_species_tool_compatibility/https://sourceforge.net/p/simulates/wiki/Walkthrough_species_tool_compatibility/Walkthrough_species_tool_compatibilityRobert KoflerTue, 25 Jul 2017 12:51:33 -0000https://sourceforge.net/p/simulates/wiki/Walkthrough_species_tool_compatibility/https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/TheClassic_SanMiguel_TELandscapeRobert KoflerTue, 25 Jul 2017 12:43:05 -0000https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/TheClassic_SanMiguel_TELandscapeRobert KoflerTue, 25 Jul 2017 12:30:26 -0000https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/https://sourceforge.net/p/simulates/wiki/Walkthrough/WalkthroughRobert KoflerTue, 25 Jul 2017 12:24:08 -0000https://sourceforge.net/p/simulates/wiki/Walkthrough/https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/describing_TE_sequencesRobert KoflerTue, 25 Jul 2017 10:15:14 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/describing_TE_sequencesRobert KoflerTue, 25 Jul 2017 10:01:12 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/describing_TE_sequencesRobert KoflerTue, 25 Jul 2017 09:52:12 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/describing_TE_landscapesRobert KoflerTue, 25 Jul 2017 09:42:16 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/describing_TE_landscapesRobert KoflerTue, 25 Jul 2017 09:36:56 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/describing_TE_landscapesRobert KoflerTue, 25 Jul 2017 09:07:44 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/describing_TE_landscapesRobert KoflerTue, 25 Jul 2017 09:04:20 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/describing_TE_landscapesRobert KoflerTue, 25 Jul 2017 09:00:15 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_landscapes/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 24 Jul 2017 15:16:25 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 24 Jul 2017 15:04:29 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 24 Jul 2017 14:48:34 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 24 Jul 2017 14:37:20 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 24 Jul 2017 14:36:41 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Manual/ManualRobert KoflerMon, 24 Jul 2017 12:11:05 -0000https://sourceforge.net/p/simulates/wiki/Manual/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerMon, 24 Jul 2017 11:55:20 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerMon, 24 Jul 2017 11:51:23 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/Home/HomeRobert KoflerMon, 24 Jul 2017 11:48:30 -0000https://sourceforge.net/p/simulates/wiki/Home/https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/describing_TE_sequencesRobert KoflerSun, 23 Jul 2017 19:54:45 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/describing_TE_sequencesRobert KoflerSun, 23 Jul 2017 19:50:38 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/describing_TE_sequencesRobert KoflerSun, 23 Jul 2017 19:50:12 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/describing_TE_sequencesRobert KoflerSun, 23 Jul 2017 19:48:29 -0000https://sourceforge.net/p/simulates/wiki/describing_TE_sequences/https://sourceforge.nethttps%3A//sourceforge.net/projects/simulates/files/releases/simulate_v1.12.zip/downloadSimulaTEThu, 20 Jul 2017 15:12:04 -0000https://sourceforge.net/projects/simulates/files/releases/simulate_v1.12.zip/downloadhttps://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/TheClassic_SanMiguel_TELandscapeRobert KoflerTue, 18 Jul 2017 12:18:01 -0000https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/TheClassic_SanMiguel_TELandscapeRobert KoflerTue, 18 Jul 2017 10:06:59 -0000https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/TheClassic_SanMiguel_TELandscapeRobert KoflerTue, 18 Jul 2017 10:05:57 -0000https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/https://sourceforge.nethttps%3A//sourceforge.net/projects/simulates/files/SanMiguel/compare-expected-observed.py/downloadSimulaTETue, 18 Jul 2017 10:01:02 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-0000https://sourceforge.net/p/simulates/wiki/TheClassic_SanMiguel_TELandscape/https://sourceforge.nethttps%3A//sourceforge.net/projects/simulates/files/SanMiguel/create-exp-ann.R/downloadSimulaTEMon, 17 Jul 2017 16:25:53 -0000https://sourceforge.net/projects/simulates/files/SanMiguel/create-exp-ann.R/downloadhttps://sourceforge.net/p/simulates/wiki/Validate_reads/Validate_readsRobert KoflerMon, 17 Jul 2017 13:31:26 -0000https://sourceforge.net/p/simulates/wiki/Validate_reads/https://sourceforge.net/p/simulates/wiki/Validate_reads/Validate_readsRobert KoflerMon, 17 Jul 2017 13:29:07 -0000https://sourceforge.net/p/simulates/wiki/Validate_reads/https://sourceforge.nethttps%3A//sourceforge.net/projects/simulates/files/validation_reads/chisquare.R/downloadSimulaTEMon, 17 Jul 2017 13:11:03 -0000https://sourceforge.net/projects/simulates/files/validation_reads/chisquare.R/downloadhttps://sourceforge.nethttps%3A//sourceforge.net/projects/simulates/files/validation_reads/kolmogorov-rld.r/downloadSimulaTEMon, 17 Jul 2017 12:51:03 -0000https://sourceforge.net/projects/simulates/files/validation_reads/kolmogorov-rld.r/downloadhttps://sourceforge.net/p/simulates/wiki/Validate_reads/Validate_readsRobert KoflerFri, 14 Jul 2017 15:01:32 -0000https://sourceforge.net/p/simulates/wiki/Validate_reads/https://sourceforge.net/p/simulates/wiki/Validate_reads/Validate_readsRobert KoflerFri, 14 Jul 2017 15:00:42 -0000https://sourceforge.net/p/simulates/wiki/Validate_reads/https://sourceforge.nethttps%3A//sourceforge.net/projects/simulates/files/validation_reads/rld-ks.R/downloadSimulaTEFri, 14 Jul 2017 14:58:03 -0000https://sourceforge.net/projects/simulates/files/validation_reads/rld-ks.R/downloadhttps://sourceforge.net/p/simulates/wiki/Walkthrough_toy/Walkthrough_toyRobert KoflerWed, 12 Jul 2017 11:45:44 -0000https://sourceforge.net/p/simulates/wiki/Walkthrough_toy/