User: skbrimer

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skbrimer610
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Posts by skbrimer

<prev • 181 results • page 1 of 19 • next >
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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 20 days ago by skbrimer610
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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 3 months ago by skbrimer610
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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 3 months ago by skbrimer610
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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 3 months ago by skbrimer610
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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 3 months ago by skbrimer610
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Answer: A: Appropriate Podcasts For A Bioinformatician?
... I like [Not So Standard Deviations][1] [1]: http://nssdeviations.com/ ...
written 4 months ago by skbrimer610
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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 4 months ago by skbrimer610
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Comment: C: Run Ray Assembler with multiple kmer values
... I do not believe that you can, SPAdes is coded with the idea that it will be comparing different kmers to find the best build. Ray is written with the idea of just one. You could try using kmergenie on your reads to see if there is an optimum kmer you should be using. ...
written 5 months ago by skbrimer610
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Answer: A: Guidance for key amino acid analysis
... You can!!!! I figured it out using biopython, seriously I can not thank them enough for making and maintaining this package. you can take your `file.aln` and read it in using biopython's `AlignIO` from there you can read it in like this align = AlignIO.read("test.aln","clustal") print(a ...
written 5 months ago by skbrimer610
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Guidance for key amino acid analysis
... Hello hive brain, We are working on an analysis at work were we are evaluating key amino acids at specific sites in a protein and I'm trying to figure out a way to speed up the analysis as this is likely something we will be doing for a while. Right now we take the processed fasta files and remove ...
alignment written 5 months ago by skbrimer610

Latest awards to skbrimer

Popular Question 12 weeks ago, created a question with more than 1,000 views. For How to get help on a question that has been buried?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Need help reading FASTQ file
Scholar 3 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 5 months ago, created a question with more than 1,000 views. For How to get help on a question that has been buried?
Popular Question 5 months ago, created a question with more than 1,000 views. For Unknown mapping difference from host removal
Popular Question 5 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Samtools 1.3 bam to fastq
Popular Question 5 months ago, created a question with more than 1,000 views. For How to get help on a question that has been buried?
Scholar 5 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 6 months ago, created a question with more than 1,000 views. For How to get help on a question that has been buried?
Appreciated 12 months ago, created a post with more than 5 votes. For A: Samtools 1.3 bam to fastq
Great Question 15 months ago, created a question with more than 5,000 views. For Samtools 1.3 bam to fastq
Popular Question 15 months ago, created a question with more than 1,000 views. For How to get help on a question that has been buried?
Popular Question 21 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Popular Question 21 months ago, created a question with more than 1,000 views. For SNP visualization with nucleotide %
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Popular Question 22 months ago, created a question with more than 1,000 views. For SOLVED***EDIT*** BioPython: how to edit a fasta file to include a large deletion
Scholar 23 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Scholar 23 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 24 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 2.0 years ago, created a question with more than 1,000 views. For SOLVED***EDIT*** BioPython: how to edit a fasta file to include a large deletion
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Bed file loading issues
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