User: Inquisitive8995

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Posts by Inquisitive8995

<prev • 55 results • page 1 of 6 • next >
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Answer: A: How to make small subset of large genotyping dataset with plink?
... Hello, If I am not wrong, you can use the --extract command in plink to do this. > To extract only a subset of SNPs, it is possible to specify a list of required SNPs and make a new file, or perform an analysis on this subset, by using the command plink --file data --extract mysnps.txt ...
written 4 weeks ago by Inquisitive899540
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Answer: A: Add string to a column of a file and retain the rest
... I think I answered my own question. It works when I use awk as given below: awk -v FS="\t" -v OFS="\t" '{print $1"/1",$2,$3,$4,$5,$6} inputfile.txt > output.txt ...
written 9 weeks ago by Inquisitive899540
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Comment: C: Exctracting genotype data on a single SNP from all individuals in a dataset
... Can you try and create a format similar to what 23andme uses? Like what is given below. `# rsid chromosome position genotype rs3094315 1 742429 AG rs12562034 1 758311 AG rs3934834 1 995669 CC` Then you can use plink to change that file to a ...
written 9 weeks ago by Inquisitive899540
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Comment: C: Add string to a column of a file and retain the rest
... Thanks for your reply. But this added the `\t` between column 1 and 2 but did not add "\1" ...
written 9 weeks ago by Inquisitive899540
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Comment: C: Add string to a column of a file and retain the rest
... Thanks for your reply but this joined the first and second column into 1. ...
written 9 weeks ago by Inquisitive899540
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Comment: C: Exctracting genotype data on a single SNP from all individuals in a dataset
... Can you show a few lines of the impute file ? ...
written 9 weeks ago by Inquisitive899540
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Comment: C: Looping over plink files
... Did you try `--merge-list` option from plink ? You can merge all the chormosomes for one file using this and do a for loop to merge with other files. http://zzz.bwh.harvard.edu/plink/dataman.shtml#mergelist ...
written 9 weeks ago by Inquisitive899540
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Add string to a column of a file and retain the rest
... Hi, I have a file with multiple rows which look like 1101:4422:200A gi|12345|ref|NC_021085.1| 100 N/A bacterium AC A78261 I want to add `/1` after the first column and keep all the other columns intact. so that the output looks like 1101:4422:200A/1 gi|12345|ref|NC_021085 ...
linux awk written 9 weeks ago by Inquisitive899540
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Comment: C: merge two SNP vcf file
... Did you try VCF tools ? They have merge option. http://vcftools.sourceforge.net/perl_module.html ...
written 10 weeks ago by Inquisitive899540
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Comment: C: NCBI edirect efetch error
... Thanks. I will try both of these ...
written 10 weeks ago by Inquisitive899540

Latest awards to Inquisitive8995

Supporter 12 weeks ago, voted at least 25 times.
Popular Question 4 months ago, created a question with more than 1,000 views. For Delete columns with specific headers in a dataframe in R
Popular Question 6 months ago, created a question with more than 1,000 views. For Delete columns with specific headers in a dataframe in R

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