Extract list of gene coordinates from gff file

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3.9 years ago

the_cowa ▴ 40

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 ?

gene gff awk grep python • 3.0k views

ADD COMMENT • link 3.9 years ago by the_cowa ▴ 40

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Try to make your regex as specific as possible. E.g. grep GSBRNA2T00155995001 sample.gtf will be slightly slower than grep 'gene_id \"GSBRNA2T00155995001' sample.gtf. How much improvement you can gain from this depends on the structure of your gtf file.

ADD REPLY • link 3.9 years ago by flappix ▴ 30

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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 grep for extracting data.

ADD REPLY • link 3.9 years ago by GenoMax 141k

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I tried with join but that is also too slow

ADD REPLY • link 3.9 years ago by the_cowa ▴ 40

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Break your gff file in several pieces and then do the search.

ADD REPLY • link 3.9 years ago by GenoMax 141k

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