User: jean.elbers
jean.elbers • 470
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Posts by jean.elbers
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... minor comment: Q20 (1 in 100) likewise Q30 (1 in 1000) ...
written 7 days ago by
jean.elbers • 470
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... You should probably use PBJelly (https://sourceforge.net/p/pb-jelly/wiki/Home/). Here are some instructions for running PBJelly for PacBio Sequel subreads and error correcting using a variant caller instead of Pilon to correct indels (https://gist.github.com/jelber2/730f8d9d05ea5bbc933d5da2c97bedea) ...
written 27 days ago by
jean.elbers • 470
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Comment:
C: How to do AMOVA on GBS data
... Presumably, you need to specify the hierarchy (structure) of your populations. Granted I haven't read the documentation for the R package or specific function. ...
written 28 days ago by
jean.elbers • 470
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Comment:
C: How to do AMOVA on GBS data
... I don't know anything about this R package or the specific function, but it looks like you need to supply an R object to `hier`. You would need to read the function's documentation. Perhaps the author(s) have a vignette or example data that you should try to see if it works with the example data. ...
written 29 days ago by
jean.elbers • 470
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Comment:
C: RepeatMasker Library Help
... I couldn't get RepeatMasker open-4.08 (RepBase 20181026) to work with MAKER 2.31.10 - did you get it to work with MAKER? I could only get RepeatMasker open-4.07 (RepBase 20170127) to work. ...
written 5 weeks ago by
jean.elbers • 470
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C: filter genome above N50 value
... There is "newer" pipeline for combining the two assemblies called NucMerge that you might try (https://www.biorxiv.org/content/early/2018/11/30/483701), but I would first consider https://www.biostars.org/p/352554/#352569 ...
written 7 weeks ago by
jean.elbers • 470
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Comment:
C: Gff3 file issues
... Is your gff3 file the output of `gff3_merge` without filtering? It appears that you have filtered to keep only `source` (i.e., 2nd column) as `maker`. Perhaps you need to redo `gff3_merge` without filtering it's output to input into JBrowse, as some features of the gff3 file seem to be missing. ...
written 7 weeks ago by
jean.elbers • 470
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... Thanks- it is fixed now. ...
written 8 weeks ago by
jean.elbers • 470
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... This might be possible with Synima (https://github.com/rhysf/Synima ). You would just restrict the input files to the region you are interested in. ...
written 8 weeks ago by
jean.elbers • 470
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... I would use the most up-to-date Swiss-Prot database
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
and not worry about combining RefSeq or transposon sequences. Someone with more experience might have better advice to give, but I ...
written 10 weeks ago by
jean.elbers • 470
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For A: What is Read Group platform??
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For A: What is Read Group platform??
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Teacher
9 months ago,
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For A: What is Read Group platform??
Scholar
10 months ago,
created an answer that has been accepted.
For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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