User: mrmrwinter
mrmrwinter • 30
- 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
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... 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 ...
written 10 months ago by
mrmrwinter • 30
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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
mrmrwinter • 30
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Comment:
C: If loop in snakemake
... Great, thank you both ...
written 10 months ago by
mrmrwinter • 30
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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
mrmrwinter • 30
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Comment:
C: If loop in snakemake
... Ok, thanks. Still new to the terminology ...
written 10 months ago by
mrmrwinter • 30
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... 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 ...
written 10 months ago by
mrmrwinter • 30
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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
mrmrwinter • 30
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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
mrmrwinter • 30
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... 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
mrmrwinter • 30
0
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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
mrmrwinter • 30
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