User: gbl1

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gbl120
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Posts by gbl1

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Answer: A: assembly on a single DNA sequence
... Hi, So, I managed to extend my elements by a long manual method (Blast and assembly), I do not have to rush anymore, but I still would like to ba able to get an assembly on a sequence from reads. So, I give the results I obtain: Initial sequence: >2-1-u Leymus arenarius predicted call ...
written 4 months ago by gbl120
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Comment: C: How to compute convergence in phylogeny in R?
... Well my package is dealing with dominant markers, but if you want to see if any function might be helpful : https://github.com/giby/Linarius/ there are a lot of protein specific computation… Try to get a ppt of a class about it… from last time I delt with it, I remember about blossum… ...
written 4 months ago by gbl120
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Comment: C: How can I remove sequences with only gaps (-) from a multi-fasta file?
... Actually, I've got another way… I need to ask the computer service… I do not have admin right on my university computer ...
written 4 months ago by gbl120
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Comment: C: How can I remove sequences with only gaps (-) from a multi-fasta file?
... indeed, formating issue... So, i tried: bash: seqkit: command not found ...
written 4 months ago by gbl120
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Comment: A: How to compute convergence in phylogeny in R?
... Phylogenetic distances are tuff on R. I made a package for my case, as nothing existed. What is your personal case? maybe I could help… What kind of marker are you using? ...
written 4 months ago by gbl120
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Comment: C: How can I remove sequences with only gaps (-) from a multi-fasta file?
... Minimal input: >M02764:85:000000000-BLWLC:1:1101:13787:1000 1:N:0:1 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ...
written 4 months ago by gbl120 • updated 4 months ago by RamRS19k
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Comment: C: assembly on a single DNA sequence
... yes, there is 16 GO of reads, that covers normally the whole genome, I think it is illumina, but not sure... Assembly is an issue in itself, I tried with MECAT, and it said for such an assembly, it would need one TB of RAM to proceed... basically, I want: let's say my sequences I want to exten ...
written 4 months ago by gbl120
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Comment: C: assembly on a single DNA sequence
... For the use of jvarkit, Here are my commands: 306 git clone "https://github.com/lindenb/jvarkit.git" 307 cd jvarkit 308 make extendrefwithreads 309 ls 310 cat README.md 311 ls 312 extendrefwithreads 313 ./extendrefwithreads 314 locate extendrefwithreads I think it is ...
written 4 months ago by gbl120
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Comment: C: How can I remove sequences with only gaps (-) from a multi-fasta file?
... How? Not obvious after RTFM of bioawk ...
written 4 months ago by gbl120
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Comment: C: assembly on a single DNA sequence
... Hi, thanks for your answer, on this wonderful sunny saturday, from my lab, here is the command: 1) I don't say he is lazy, I know he is hard working, and competant. I just say he, like many informaticists, want to do things in the most elegant way, that is time and resource costly, and sometime ...
written 4 months ago by gbl120

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