sort the homo sapiens genes by chromosome with Unix command lines

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6.5 years ago

Huichen03 ▴ 40

Hi,

I want to sort homo sapiens gene by chromosome. I tried with sort -t _ -k 3 -g genes.txt > genes_by_chr.txt, while the result is not what I want. In my genes.txt file, the chromosome column includes numbers like 1, 2, 3 ... and characters like CHR_HG1_PATCH, CHR_HG26_PATCH, and GL000009.2. What is the easiest way to sort my genes by chromosome, if I only use Unix commands?

Thank you in advance!

gene sort • 1.5k views

ADD COMMENT • link 6.5 years ago by Huichen03 ▴ 40

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How about sort -kz,z genes.txt > genes_by_chr.txt, where z is the column of interest. In case you have positional information for your genes, you may add -kx,xn, where x is the column of the genomic coordinate and "n" indicates to sort numerically.

ADD REPLY • link 6.5 years ago by ATpoint 85k

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Paste add some example data, in additon to data description. Data description is good, but it is more helpful if you can post some example data.

try sort -V -k1 if chromsomes are in first column.

ADD REPLY • link 6.5 years ago by cpad0112 21k

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