User: skbrimer

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skbrimer650
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650
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United States
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2 months, 3 weeks ago
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6 years, 2 months ago
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Posts by skbrimer

<prev • 184 results • page 1 of 19 • next >
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Answer: A: Snakemake input error with files from inconsistent naming scheme
... So here is the solution I figured out. rule minimap2: input: "{sample}_strict" params: suffix=lambda wildcards: config["barcodes"][wildcards.sample] output: "{sample}.bam" shell: "minimap2 -ax map-ont -t8 ../consen ...
written 5 months ago by skbrimer650
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Snakemake input error with files from inconsistent naming scheme
... Hello hive brain, I am trying to make a workflow in snakemake to process some MinION reads. they are cDNA amplicons of different genotypes of the same virus that were multiplex together. To make sure that I am only using the barcodes I want to be using I am pre-processing the reads with porechop t ...
cdna minion snakemake nanopore written 5 months ago by skbrimer650
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Answer: A: How to merge gff3 files?
... if you are using a linux machine can you not just `cat *.gff > superbanana.gff` I think that should work, the gff files I have worked with in the past didn't have headers so I don't think there is an issue there. Also there is this thread https://www.biostars.org/p/69562/ ...
written 8 months ago by skbrimer650
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Comment: C: How to remove features from GBK files with biopython ?
... Can you post on the genbank accession number for the file you are playing with so we can test some code? ...
written 13 months ago by skbrimer650
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Answer: A: loading yaml file into snakemake
... Here is my solution to this and I hope it helps other people who are just starting with Snakemake. Thank you again Wouter for the input and examples! configfile: "config.yaml" print("Starting amplicon analysis workflow") rule all: input: expand("data/{sampl ...
written 16 months ago by skbrimer650
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Comment: C: loading yaml file into snakemake
... So it has taken a day but I did get it to work and I think I understand why it works now as well. The `config.yaml` file gets imported in a python dictionary, but the format for the sample location makes it a nest dictionary. So you have to use the `expand("{sample}", sample = config["samples"])` no ...
written 16 months ago by skbrimer650
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Comment: A: loading yaml file into snakemake
... Thank you for the feedback Wouter! I will give this a try when I escape the lab today ...
written 16 months ago by skbrimer650
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loading yaml file into snakemake
... Hello hive mind, I'm having issues moving snakemake from one sample to multiple samples. I have gotten this workflow to work for processing amplicon targets and it worked great. rule all: input: "data/samples/LS19-3433-21_s1_de_novo" rule seqtk_qualtiy_filter: ...
software error assembly written 16 months ago by skbrimer650
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Answer: A: Appropriate Podcasts For A Bioinformatician?
... I like [Not So Standard Deviations][1] [1]: http://nssdeviations.com/ ...
written 16 months ago by skbrimer650
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Answer: A: pysam alignment error
... I have not used pysam before but have you tried the suggestion the code gives `samfile = pysam.AlignmentFile(os.path.join(path,bam), check_sq=False, 'rb')` ? also are you using Windows to process the file the `rb` call is for windows, linux/mac would be just `r` ...
written 16 months ago by skbrimer650

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