User: mrmrwinter

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Posts by mrmrwinter

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Order assignment given family and genus level in R
... Yes automatically using a package. I have a .csv, of which one column is a list of species names, another is a list of family names etc. I want to add a column that has the Order of each of these entries. Ive done some molecular taxonomic assignment before, so i know these things are possible, but ...
written 18 days ago by mrmrwinter0
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Order assignment given family and genus level in R
... I have a .csv with various anatomical measurements of animals. Each of these entries also has family/genus/species level classification. I want some way to assign Order to each of these entries, within R. Is there a package for this in R? Or am i going to have to do it in python etc? Thanks ...
R taxomonic assignment transformation written 18 days ago by mrmrwinter0
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Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... I'm installing JBrowse as i type Thanks again Juke ...
written 10 weeks ago by mrmrwinter0
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Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... Does overtraining result in fewer predictions then? Does this mean i should take the results of an earlier iteration? One nearer what would be expected? ...
written 10 weeks ago by mrmrwinter0
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Less and less genes predicted with each iteration of SNAP/MAKER
... Hi I am annotating a de novo genome using MAKER. I first ran maker with est and protein information from a closely related species, with est2genome and protein2genome on. I then ran MAKER with SNAP switched on, using the output of the previous step as input for snap I then ran MAKER with SNAP sw ...
annotation gene prediction snap genomics maker written 10 weeks ago by mrmrwinter0
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Comment: C: If loop in snakemake
... Maybe im not explaining it well enough. "the outputs of two rules are the same wildcard/file, results/rereplicated/{library}/{sample}.fasta, and this raises an ambiguity error" It is not trying to have two files with the same filename in the same folder, the wildcards will be different. Ie, `res ...
written 12 weeks ago by mrmrwinter0
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Comment: C: If loop in snakemake
... Great, thank you both ...
written 12 weeks ago by mrmrwinter0
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Comment: C: If loop in snakemake
... Hi, this doesnt work; the rules already have different names The problem is that the outputs of two rules are the same wildcard/file, `results/rereplicated/{library}/{sample}.fasta`, and this raises an ambiguity error ...
written 12 weeks ago by mrmrwinter0
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Comment: C: If loop in snakemake
... Ok, thanks. Still new to the terminology ...
written 12 weeks ago by mrmrwinter0
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If loop in snakemake
... Hi im currently trying to write an if loop to use in a snakemake rule The code for the rule is as follows: rule empty_fasta_workaround: input: "results/02_trimmed/{library}/{sample}.merged.tmp.derep.fasta" output: denoise = "results/02_trimmed/{library ...
loop else snakemake shell if written 12 weeks ago by mrmrwinter0

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