User: mrmrwinter

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

Posts by mrmrwinter

<prev • 32 results • page 2 of 4 • next >
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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 months ago by mrmrwinter30
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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 10 months ago by mrmrwinter30
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Comment: C: If loop in snakemake
... Great, thank you both ...
written 10 months ago by mrmrwinter30
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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 10 months ago by mrmrwinter30
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Comment: C: If loop in snakemake
... Ok, thanks. Still new to the terminology ...
written 10 months ago by mrmrwinter30
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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 10 months ago by mrmrwinter30
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Comment: C: Counting CDS's in Maker output
... I didnt set est2genome and protein2genome on (see my other comment) `grep` finds no instances of `maker` in the `maker_mix.gff` file ...
written 10 months ago by mrmrwinter30
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Comment: C: Counting CDS's in Maker output
... This is exactly what i've done.... I was so sure i'd set them i didn't think to check. Rerunning now. Thanks for all the help ...
written 10 months ago by mrmrwinter30
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Answer: A: I want to assembly all the reads at ones in linux
... In Snakemake: sample = glob_wildcards("path/{sample}.F.fastq.gz") rule all: input: expand("path/spades_out/{sample}/scaffolds.fa", sample=sample) rule spades: input: F = "path/{sample}.F.fastq.gz" R = "path/{sample}.R.fastq.gz" ...
written 10 months ago by mrmrwinter30
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Comment: C: Counting CDS's in Maker output
... Im running MAKER 2.31. I wasnt aware there was a MAKER3. I am installing it through bioconda though, which may be causing issues. And no, im running it on a Centos HPC. `awk '{if ($3 == "CDS") a++}END{print a}' maker_mix.gff` didnt work, and a quick grep count for "CDS" came back with 0, but the f ...
written 10 months ago by mrmrwinter30

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