I am using agat atm to convert a gff file to bed using the following command.
agat_convert_sp_gff2bed.pl -gff Arabidopsis_thaliana_TAIR10.gff3 -o test.bed
When I convert the gff to bed I find NA values (aka .) in the thickStart and thickEnd column of the bed file for the non-coding RNAs.
Is there a way to convert gff to bed and acquire a thickStart and thickEnd values for these elements?
Thank you for your time
In the link, I post the gff3 file that I am working on https://drive.google.com/drive/folders/1-wmbc9gKtbXFJ95E0n41WgPL-G313SNe?usp=sharing
1 answer
thickStart and thickEnd are usulally used to define coding part (CDS), which does not exist for non-coding genes.
A possibility is to fill thickStart and thickEnd with chromStart and chromEnd values using a awk command:
awk 'BEGIN{OFS="\t"}{if($7 == "."){$7=$2; $8=$3} print $0 }' file.bed
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