User: mrmrwinter

gravatar for mrmrwinter
mrmrwinter30
Reputation:
30
Status:
New User
Location:
University of Hull
Website:
https://github.com/mrm...
Twitter:
@mrmrwinter
Last seen:
3 months, 1 week ago
Joined:
1 year, 5 months ago
Email:
m*********@gmail.com

Posts by mrmrwinter

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Combining nanopore libraries
... Awesome, thanks. This is exactly what i needed ...
written 3 months ago by mrmrwinter30
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Combining nanopore libraries
... Hi I have two PromethION libraries, one standard, and the other with ultralong read chemistry. To create a draft assembly i pooled the fastqs of both libraries and assembled from the result. Now i am coming to nanopolishing the assembly and it requires the fast5 signal files of reads used in the ...
assembly nanopore promethion written 3 months ago by mrmrwinter30 • updated 3 months ago by colindaven2.6k
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Comment: A: Best open source genome browser in 2020
... Thanks all. I'm going with IGV ...
written 3 months ago by mrmrwinter30
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Forum: Best open source genome browser in 2020
... What in your opinion are the bet open source genome browsers available now? I have used several including JBrowse, Genome Workbench, and Artemis, but find them all clunky and their GUIs dated. Genious looks very good, but its licence requirement limits distribution of results and outputs, and is r ...
genome browser forum genomics bioinformatics written 3 months ago by mrmrwinter30 • updated 12 weeks ago by Carlo Yague5.7k
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Which ete3 format to parse a newick file with concordance values?
... Hi I am trying to plot several trees in toytree but it is returning an error. `Unexpected newick format 100/48.8/63.1:0.0045539444` The tree was made in IQTREE using the -gcf and -scf commands to calculate and apply concordance factors as support values. I have checked the documentation of iqtre ...
phylogenetics iqtree newick concordance factors written 7 months ago by mrmrwinter30
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Allow for failed wildcards in Snakemake workflow
... Hi, I have a snakemake workflow that contains a small section with several shell command rules and external python script rules. The rules iterate over a wildcard, {OG}, which is created at the beginning of the workflow. At each rule, some of the wildcards will fail. The successful ones should be ...
python snakemake wildcards written 7 months ago by mrmrwinter30
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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 9 months ago by mrmrwinter30
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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 9 months ago by mrmrwinter30
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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 11 months ago by mrmrwinter30
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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 11 months ago by mrmrwinter30

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