Bedtools Slop for Specific Features
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5.6 years ago
gtasource ▴ 60

I want to use Bedtools Slop on a GTF file, but only on specific features (for example only for those labeled as gene, or exon, ect.)

I have been trying to pipeline the command with awk, but to no avail:

awk '{ if ($3 == "gene") | bedtools slop -i A.bed -g my.genome -l 2 -r 3

Any help would be great!

bedtools awk • 1.4k views
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1
Entering edit mode
5.6 years ago
Jeffin Rockey ★ 1.3k

Please give it like below

awk '$3=="gene"{print}' my.gtf | bedtools slop -i -  -g my.genome  -l 2 -r 3
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