https://sourceforge.net/p/bio-rainbow/activity/Recent activity for rainbowenThu, 21 Sep 2017 17:30:17 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/34cd1284/?limit=25#9541Hi Catalina, You're correct. After the div step, you should get a very strict haplotype. But I don't know if the length of the haplotype meets your need. In addition, the divided clusters may not come from the same locus since the clustering may involve similar sequences of different loci. Thanks, ZechenZechen ChongThu, 21 Sep 2017 17:30:17 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/34cd1284/?limit=25#9541https://sourceforge.net/p/bio-rainbow/discussion/general/thread/34cd1284/?limit=25#98d5Hi Zechen! I am trying to use the heterozygosity as and additional source of information from a RADseq dataset and I want to know if I can get the phased haplotypes while implementing Rainbow. As far as I understand, the heterozygous sequences are collapsed during the "Bottom–up merging process" (rainbow merge), but I wanted to know if there is a way to obtain the different haplotypes for each locus at any point? According to the paper, the dividing procedure (top–down dividing clusters - rainbow...Catalina Ramirez-PortillaThu, 21 Sep 2017 15:56:14 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/34cd1284/?limit=25#98d5https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#3f27Hi Zechen, many thanks for your clarification! I have also noticed that when the...Claudius KerthSat, 22 Oct 2016 17:59:47 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#3f27https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#274e/059bHi Claudius, The first two are correct. The third one is strand, i.e. , forward or...Zechen ChongSat, 22 Oct 2016 09:45:01 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#274e/059bhttps://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#274eHi Zechen, I think I understand now what the numbers in the lines starting with R...Claudius KerthSat, 22 Oct 2016 09:39:57 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#274ehttps://sourceforge.net/p/bio-rainbow/discussion/general/thread/f6d194c9/?limit=25#bb0eHi Zechen, I have found the reason for the odd behaviour of rainbow div. The input...Claudius KerthFri, 21 Oct 2016 22:19:53 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/f6d194c9/?limit=25#bb0ehttps://sourceforge.net/p/bio-rainbow/discussion/general/thread/f6d194c9/?limit=25#7dddHi Zechen, I have problems with the output of rainbow div. I have run it with -k...Claudius KerthFri, 21 Oct 2016 09:57:22 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/f6d194c9/?limit=25#7dddhttps://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#68b0Hi Zechen, @me: RTFD. Sorry! However, the readID's are not fully clear to me. What...Claudius KerthFri, 21 Oct 2016 09:13:00 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#68b0https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#c33b/c3b0Hi Claudius, There is a description in the README file. Will it meet your need? Thanks,...Zechen ChongTue, 18 Oct 2016 20:15:07 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#c33b/c3b0https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#c33bHi Zechen, I am struggling to make sense of the output format of rbasm. Do you have...Claudius KerthMon, 17 Oct 2016 07:19:51 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/bd346a5f/?limit=25#c33bhttps://sourceforge.net/p/bio-rainbow/discussion/general/thread/1a9dfaed/?limit=25#ee03Dear Claudius, Thanks for trying rainbow. Yes, you are right. The merge step is also...Claudius KerthMon, 17 Oct 2016 06:54:56 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/1a9dfaed/?limit=25#ee03https://sourceforge.net/p/bio-rainbow/discussion/general/thread/1a9dfaed/?limit=25#7c4aDear Mr Chong, I have a question regarding your programme Rainbow. I am not sure...Claudius KerthMon, 03 Oct 2016 10:52:17 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/1a9dfaed/?limit=25#7c4ahttps://sourceforge.nethttp%3A//sourceforge.net/projects/bio-rainbow/files/rainbow_2.0.4.tar.gz/downloadrainbowMon, 03 Aug 2015 15:51:02 -0000http://sourceforge.net/projects/bio-rainbow/files/rainbow_2.0.4.tar.gz/downloadhttps://sourceforge.net/p/bio-rainbow/code/ci/5b0b3d57d68fc7ff0f2c714ef799608ac1e918b0/added ezmsim moduleZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/5b0b3d57d68fc7ff0f2c714ef799608ac1e918b0/https://sourceforge.net/p/bio-rainbow/code/ci/1d47912bdd4314c18887fe09597af16a26bc8306/added index_ctgs and free_indexZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/1d47912bdd4314c18887fe09597af16a26bc8306/https://sourceforge.net/p/bio-rainbow/code/ci/269de915322fa7e203fb18d20ccb32d4c9b17f06/modified: MakefileZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/269de915322fa7e203fb18d20ccb32d4c9b17f06/https://sourceforge.net/p/bio-rainbow/code/ci/dea8003ad7d6a2286493c14a81e250f6bce62992/new file: .gitignoreZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/dea8003ad7d6a2286493c14a81e250f6bce62992/https://sourceforge.net/p/bio-rainbow/code/ci/6293472bac5127ffccb4cd28b1cf49407b78cd16/ modified: divide.cZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/6293472bac5127ffccb4cd28b1cf49407b78cd16/https://sourceforge.net/p/bio-rainbow/code/ci/7e27e3590a1843f63088772e1969afa6ec691d13/ modified: mergectg.cZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/7e27e3590a1843f63088772e1969afa6ec691d13/https://sourceforge.net/p/bio-rainbow/code/ci/c40a9f0854ac5b1c17106babc26e9db265079c79/just comparing reads similarity between two clu...Zechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/c40a9f0854ac5b1c17106babc26e9db265079c79/https://sourceforge.net/p/bio-rainbow/code/ci/0364abc1762ccbe5dc55bfe9381fabfa35a3aa7f/new file: .gitignoreZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/0364abc1762ccbe5dc55bfe9381fabfa35a3aa7f/https://sourceforge.net/p/bio-rainbow/code/ci/5f24641a7619bfd3d8d9b02a396bea366e3fa5f0/rainbow1.1Zechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/5f24641a7619bfd3d8d9b02a396bea366e3fa5f0/https://sourceforge.net/p/bio-rainbow/code/ci/4460b0b60d20ea975f30664e29093837c091dc2b/ modified: divide.cZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/4460b0b60d20ea975f30664e29093837c091dc2b/https://sourceforge.net/p/bio-rainbow/code/ci/8b6aa4d298657bfd6ed1071085808c7ee0c6ae2e/seedup divide moduleZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/8b6aa4d298657bfd6ed1071085808c7ee0c6ae2e/https://sourceforge.net/p/bio-rainbow/code/ci/da5cc0ff7e2c3fbd9bc7a0a0263a6052871a7cad/Makefile changedZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/da5cc0ff7e2c3fbd9bc7a0a0263a6052871a7cad/https://sourceforge.net/p/bio-rainbow/code/ci/0738b3a7d14aec97508d36e36f89aa55350d0689/update README.txt and rerun_rbasm.plZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/0738b3a7d14aec97508d36e36f89aa55350d0689/https://sourceforge.net/p/bio-rainbow/code/ci/e12d6838fd809df46499c25e6dc584b3d750a594/modified MakefileZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/e12d6838fd809df46499c25e6dc584b3d750a594/https://sourceforge.net/p/bio-rainbow/code/ci/5941287ebb44ab6fb1d3936e0b28f3b364701167/prepare ctgs to merge doneZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/5941287ebb44ab6fb1d3936e0b28f3b364701167/https://sourceforge.net/p/bio-rainbow/code/ci/a66f4efb1d621b9c3ea35c418dfb58e0ddeffe03/merge and assemble along tree and hash all leavesZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/a66f4efb1d621b9c3ea35c418dfb58e0ddeffe03/https://sourceforge.net/p/bio-rainbow/code/ci/de4d120851267469d55a57818c8ae665de0a3b07/modified: mergectg.cZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/de4d120851267469d55a57818c8ae665de0a3b07/https://sourceforge.net/p/bio-rainbow/code/ci/a380c5d6b2af1aae0003cd588761266523f679c3/ modified: main.cZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/a380c5d6b2af1aae0003cd588761266523f679c3/https://sourceforge.net/p/bio-rainbow/code/ci/9801cb1aa2908cebbc10605e62a8d197709c0bc0/divide using call_key_col instead of _call_key_colZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/9801cb1aa2908cebbc10605e62a8d197709c0bc0/https://sourceforge.net/p/bio-rainbow/code/ci/f9d82210f720cf4ac0d72475b91db30345dc671a/new file mergectg.h mergectg.cZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/f9d82210f720cf4ac0d72475b91db30345dc671a/https://sourceforge.net/p/bio-rainbow/code/ci/f91df3e456b35a34c33e5edd8c9f248aa195558c/modified: MakefileZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/f91df3e456b35a34c33e5edd8c9f248aa195558c/https://sourceforge.net/p/bio-rainbow/code/ci/a96385b3da89a559542323c6fce35d3107d415d6/rainbow 2.0.2Zechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/a96385b3da89a559542323c6fce35d3107d415d6/https://sourceforge.net/p/bio-rainbow/code/ci/875f03a2351cd7928b5c089a615ea2bd34fbb74c/ modified: MakefileZechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/875f03a2351cd7928b5c089a615ea2bd34fbb74c/https://sourceforge.net/p/bio-rainbow/code/ci/ac565e1dcc7606d59f96b576d4ae3716a320c6a8/tree guided merge ctgs done! version 1.2Zechen ChongTue, 28 Jul 2015 15:07:26 -0000https://sourceforge.net/p/bio-rainbow/code/ci/ac565e1dcc7606d59f96b576d4ae3716a320c6a8/https://sourceforge.net/p/bio-rainbow/code/ci/1d4bf19229eb9a703dd890f557cd5facfbc004e4/make a few changes compatible with UbuntuZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/1d4bf19229eb9a703dd890f557cd5facfbc004e4/https://sourceforge.net/p/bio-rainbow/code/ci/83010d65d90fdf84042176a29681bf7930d6f2c2/merged with originZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/83010d65d90fdf84042176a29681bf7930d6f2c2/https://sourceforge.net/p/bio-rainbow/code/ci/d86b801020603ca7a4bfb75aab0030f4bfc6d3f1/ modified: README.txtZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/d86b801020603ca7a4bfb75aab0030f4bfc6d3f1/https://sourceforge.net/p/bio-rainbow/code/ci/1831d75903a4fb0dd1881231e8e9fe33df0676a5/ modified: divide.cZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/1831d75903a4fb0dd1881231e8e9fe33df0676a5/https://sourceforge.net/p/bio-rainbow/code/ci/80572c69dea52e6db761879685a57fe6f36b2cc9/Merge branch 'rjdiv'Zechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/80572c69dea52e6db761879685a57fe6f36b2cc9/https://sourceforge.net/p/bio-rainbow/code/ci/684d4b8182b016528ff2e5f3d5cc5a767ea0a7c0/ new file: bloom_filter.hZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/684d4b8182b016528ff2e5f3d5cc5a767ea0a7c0/https://sourceforge.net/p/bio-rainbow/code/ci/4949f1887ae25835f58f04c0cf309ed35872c64a/ modified: divide.cZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/4949f1887ae25835f58f04c0cf309ed35872c64a/https://sourceforge.net/p/bio-rainbow/code/ci/013457d18e546eeceb748e599a96f4ec0dce2b9f/ modified: divide.cZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/013457d18e546eeceb748e599a96f4ec0dce2b9f/https://sourceforge.net/p/bio-rainbow/code/ci/110782c219da59109dda328732db4e3ba67a8220/ modified: asm_R2.cZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/110782c219da59109dda328732db4e3ba67a8220/https://sourceforge.net/p/bio-rainbow/code/ci/6ad5255271ca5b790de723e5ac370ed6831a5dac/add select_all_rbcontig.pl to fetch all contigs...Zechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/6ad5255271ca5b790de723e5ac370ed6831a5dac/https://sourceforge.net/p/bio-rainbow/code/ci/060495c713f54cd15e08883680910f8a52d5159c/ modified: mergectg.cZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/060495c713f54cd15e08883680910f8a52d5159c/https://sourceforge.net/p/bio-rainbow/code/ci/55f638fb145c62f92fa7ac86b865d99ed2e72d8d/modified: mergectg, memory pool was usedZechen ChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/55f638fb145c62f92fa7ac86b865d99ed2e72d8d/https://sourceforge.net/p/bio-rainbow/code/ci/d83ead55d092d20d79f1805ac464726a98f5b73c/ On branch masterChongTue, 28 Jul 2015 15:07:25 -0000https://sourceforge.net/p/bio-rainbow/code/ci/d83ead55d092d20d79f1805ac464726a98f5b73c/https://sourceforge.net/p/bio-rainbow/discussion/general/thread/f29dda20/?limit=25#93c8/b4d8Hi Alex, Thanks for pointing this out. I have fixed this. You can install rainbow...Zechen ChongMon, 27 Jul 2015 19:41:01 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/f29dda20/?limit=25#93c8/b4d8https://sourceforge.net/p/bio-rainbow/discussion/general/thread/f29dda20/?limit=25#93c8I got a 403 trying to open a ticket, so here we are: Rainbow 2.0.2 and 2.0.3 fail...AlexSun, 26 Jul 2015 00:27:00 -0000https://sourceforge.net/p/bio-rainbow/discussion/general/thread/f29dda20/?limit=25#93c8