Extract list of gene coordinates from gff file
I have a list of genes and I need coordinates of those genes from the gff file.
I tried with
grep -wFf gene_list sample.gff
but it is taking too much time to respond (size of gff file is 20GB). Is there any other way to extract coordinates ?
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the_cowa •
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If @Pierre's answer worked for you in this: Bed file grepping from the list have you tried to use it here? BTW, programs written in python etc are not likely to be faster than a system utility like
grepfor extracting data.I tried with join but that is also too slow
Break your gff file in several pieces and then do the search.
Try to make your regex as specific as possible. E.g.
grep GSBRNA2T00155995001 sample.gtfwill be slightly slower thangrep 'gene_id \"GSBRNA2T00155995001' sample.gtf. How much improvement you can gain from this depends on the structure of your gtf file.