Activity for rainbow
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Zechen Chong posted a comment on discussion General Discussion
Hi 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, Zechen
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Catalina Ramirez-Portilla posted a comment on discussion General Discussion
Hi 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...
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Claudius Kerth posted a comment on discussion General Discussion
Hi Zechen, many thanks for your clarification! I have also noticed that when the...
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Hi Claudius, The first two are correct. The third one is strand, i.e. , forward or...
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Hi Zechen, I think I understand now what the numbers in the lines starting with R...
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Hi Zechen, I have found the reason for the odd behaviour of rainbow div. The input...
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Hi Zechen, I have problems with the output of rainbow div. I have run it with -k...
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Hi Zechen, @me: RTFD. Sorry! However, the readID's are not fully clear to me. What...
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Hi Claudius, There is a description in the README file. Will it meet your need? Thanks,...
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Hi Zechen, I am struggling to make sense of the output format of rbasm. Do you have...
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Dear Claudius, Thanks for trying rainbow. Yes, you are right. The merge step is also...
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Dear Mr Chong, I have a question regarding your programme Rainbow. I am not sure...
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rainbow released /rainbow_2.0.4.tar.gz
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added ezmsim module
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added index_ctgs and free_index
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modified: Makefile
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new file: .gitignore
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modified: divide.c
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modified: mergectg.c
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just comparing reads similarity between two clu...
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new file: .gitignore
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rainbow1.1
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modified: divide.c
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seedup divide module
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Makefile changed
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update README.txt and rerun_rbasm.pl
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modified Makefile
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prepare ctgs to merge done
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merge and assemble along tree and hash all leaves
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modified: mergectg.c
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modified: main.c
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divide using call_key_col instead of _call_key_col
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new file mergectg.h mergectg.c
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modified: Makefile
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rainbow 2.0.2
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modified: Makefile
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tree guided merge ctgs done! version 1.2
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make a few changes compatible with Ubuntu
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merged with origin
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modified: README.txt
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modified: divide.c
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Merge branch 'rjdiv'
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new file: bloom_filter.h
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modified: divide.c
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modified: divide.c
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modified: asm_R2.c
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add select_all_rbcontig.pl to fetch all contigs...
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modified: mergectg.c
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modified: mergectg, memory pool was used
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Chong committed [d83ead]
On branch master
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Hi Alex, Thanks for pointing this out. I have fixed this. You can install rainbow...
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Alex posted a comment on discussion General Discussion
I got a 403 trying to open a ticket, so here we are: Rainbow 2.0.2 and 2.0.3 fail...
