User: jespinoz

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jespinoz20
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Posts by jespinoz

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Is there a list of E. coli genes whose promoters use sigma factor 70 (sigma70)?
... I've only seen things like this which are difficult to mine: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0090447.s002&type=supplementary ...
written 20 months ago by jespinoz20
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Is there a list of E. coli genes whose promoters use sigma factor 70 (sigma70)?
... I have a list of *E. coli* gene IDs with mappings between KEGG/BLATTNER and EcoCyc. I want to know which of these genes use the main sigma factor. **Is there a "data-science friendly" table that I could use** (e.g. tsv,csv, or excel compared to PDF)? Is this information in a database that could b ...
e. coli rna-seq genomics sigma transcription written 20 months ago by jespinoz20
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What Blosum matrix to use for ortholog table?
... I want to create a protein ortholog table between Arabidopsis thaliana and an algae. I'm wondering what the best blosum matrix to use for this task would be. I'm using blosum50 right now but I'm not sure if there is a more appropriate one for organisms that are this divergent. ...
genome phylogeny ortholog blosum written 21 months ago by jespinoz20
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Comment: C: How to build HMM from position weight matrix?
... Interesting, I will check this out. I wasn't thinking about the additional fields that are left out of a probability matrix. I was naively using the terminology. So I need to have emission and transition state probabilites for a position weight matrix? ...
written 21 months ago by jespinoz20
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How to build HMM from position weight matrix?
... Is there a way to convert a position weight matrix into a HMM that I can use with HMMER. I have a (n,m) matrix where each n_i is a position along the motif, each m_j is a nucleotide in {A, T, C, G}, and each i,j is the probability nucleotide m_j occurring at n_i. For example, the following woul ...
motif meme hmm pwm written 21 months ago by jespinoz20
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Comment: C: How to fill in missing fields on a VCF to convert into a genotype matrix?
... I used samtools mpileup. How can I genotype them? I have all of the bam files still. ...
written 2.3 years ago by jespinoz20
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How to fill in missing fields on a VCF to convert into a genotype matrix?
... My VCF file looks like the screenshot below and I believe it is missing the necessary fields to convert it into a genotype matrix that I can actually use. It's 14GB and contains 88 samples. **How can I fill the missing fields (e.g. GT) and convert it into a genotype matrix with exact commands?** ...
vcf matrix snps bcf genotype written 2.3 years ago by jespinoz20
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Comment: C: GT and GL fields in VCF file
... How can I add missing fields? My fields are: I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MQ0F=0;MQSB=1;SGB=-0.379885;RPB=1;MQB=1;BQB=1;DP=25;QS=1,0,0.5 ...
written 2.3 years ago by jespinoz20
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Comment: C: How to convert vcf file into data matrix for machine-learning?
... I got GATK to run. I am trying to convert it into a genotype matrix. ...
written 2.3 years ago by jespinoz20
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Comment: C: remove private alleles from a vcf file
... Is MAF minimum or maximum allele frequency and what would I set it at for 88 samples? ...
written 2.3 years ago by jespinoz20

Latest awards to jespinoz

Scholar 2.3 years ago, created an answer that has been accepted. For A: Cannot merge BCF files with `bcftools` files because "Index required, expected .

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