https://divingintogeneticsandgenomics.com/tags/grep/ Recent content in Grep on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Wed, 22 Oct 2014 06:40:00 -0700 https://divingintogeneticsandgenomics.com/archive/speed-up-grep/ Wed, 22 Oct 2014 06:40:00 -0700 https://divingintogeneticsandgenomics.com/archive/speed-up-grep/ I had a list of gene names in txt file. There are around 500 genes with one gene name in one line, and I want to filter the gtf file from ensemble Homo_sapines.GRCh37.74gtf.gz the gtf file contains 2244857 lines. I used grep to do it, but it takes very long (~1 hour). what I used: zcat Homo_sapines.GRCh37.74gtf.gz | grep -f gene_names.txt -w > my_genes.gtf I searched on line, and found several posts in stackoverflow to speed up grep: