User: gary.napier

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gary.napier20
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Posts by gary.napier

<prev • 22 results • page 1 of 3 • next >
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How to get the gene name/region from a list of positions
... I have a list of SNP positions: ``` 761155 4402247 472711 4027247 2867693 ``` I have a gff reference annotation file and a reference fasta file. How do I simply find the gene name and locus (e.g. "ctpJ", "Rv3743c", respectively; or "Rv3760", "Rv3760" if there is no gene name) where these SNPs o ...
gene snp written 4 months ago by gary.napier20 • updated 3 months ago by aroso4910
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Answer: C: How to populate a column with binary values, depending on whether a sample is pr
... Thanks. Took a while to work out, but the specific code I needed was ```plink --bfile --make-bed --make-pheno .txt '*' -aec``` ...
written 6 months ago by gary.napier20
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How to populate a column with binary values, depending on whether a sample is present in another file - bash
... I'm trying to populate the sixth column of a .fam file, as outlined here: https://www.cog-genomics.org/plink/1.9/formats#fam The column has to be binary ('1' or '2') depending on the case/control status. ('1' is control, '2' is case) I have the .fam file with all of my samples, but the case/contr ...
merging plink bash written 6 months ago by gary.napier20 • updated 6 months ago by ATpoint40k
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Comment: C: What is the statistical test for comparing the frequencies of variables in multi
... Thanks, so I tried this but there were a couple of problems, but I think I found a solution. I put the data in a table using ```table()```. When I run fisher.test() I get an error ```FEXACT error 6. LDKEY=617 is too small for this problem...```. Something to do with memory. I subsetted the table an ...
written 6 months ago by gary.napier20
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What is the statistical test for comparing the frequencies of variables in multiple groups?
... I have data that contains the occurrences of genes in different lineages: ``` Lineage Gene Gene_function 1 x regulatory proteins 1 p cell wall 1 y conserved hypotheticals 1 x respiration 1 z respiration 2 w cell wall 2 a cell wall 2 y regulatory proteins 3 b respiration 3 x cons ...
group comparison statistics written 6 months ago by gary.napier20 • updated 6 months ago by Hugo290
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Comment: C: How to split a string and swap the result in bash
... Great, thanks. I have a couple of questions though - 1) it seems to fail where I have 'stop lost' annotations: ```75*>75Q``` I presume this is because the * appears just before the >. 2) Do you know how I can do this in-place in the original file/table? For example the first two rows look ...
written 6 months ago by gary.napier20
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How to split a string and swap the result in bash
... I have a column which is the output of an annotation command (```bcftools query -f '%POS\t%REF\t%ALT\t%BCSQ\n' ```) The column I'm interested in is the amino acid position and amino acid change for SNPs, like so: ```402Y>402H``` How can I use bash code to swap these two around (if it contains ...
string text split bash written 6 months ago by gary.napier20 • updated 6 months ago by wm490
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Answer: A: How to pull from a file of positions in bcftools view
... I figured it out - ``` awk '{print "Chromosome\t"$1-1"\t"$1}' .txt | \ bcftools view -T - .vcf.gz | ... etc``` ...
written 6 months ago by gary.napier20
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How to pull from a file of positions in bcftools view
... I have some code to pull specific SNP positions from ```bcftools view``` , which I then annotate and apply ```bcftools query```, like this: ```bcftools view .vcf.gz Chromosome:123456 | bcftools csq -f .fa -g .gff | bcftools query -f '%POS\t%REF\t%ALT\t%BCSQ\n'``` How do I give the first ```bcftoo ...
bcftools subsetting written 6 months ago by gary.napier20 • updated 6 months ago by Pierre Lindenbaum131k
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Comment: C: Quick way of returning list of positions from vcf file with bcftools query
... Thanks for the suggestion, but it doesn't seem to be any quicker unfortunately. My file is huge, so I guess this is to be expected! ...
written 7 months ago by gary.napier20

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