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conversion of gff to bed file

Hello,

I want to convert a gff file to a bed file. I used:

gff2bed < sample.gff > sample.bed

I want to keep four columns in the output file in the order of gene_name chromosome start_position end_position However, after the conversion and some manual steps to keep first four columns and reordering the columns, I am getting same names multiple times with same positions such as:

V_06g024400.1   Vch06   21881   22007
V_06g024400.1.1 Vch06   21881   22007
V_06g024400.1.1:cds Vch06   21881   22007
V_06g024400.1.1:exon:2  Vch06   21881   22007

I also want to add column names as gene_name chromosome start_position end_position. Is there any way to keep unique positions only and to avoid these manual changes to the file in order to get the desired output. Thank you!

sequencing
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written by evafinegan • evafinegan

However, after the conversion and some manual steps to keep first four columns and reordering the columns

Can you describe in detail what you did?

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written by rpolicastro rpolicastro

I used:

gff2bed < sample.gff > sample.bed
cut -f 1-4 sample.bed > sample_1.bed
awk 'BEGIN {FS="\t"; OFS=","} {print $4, $1, $2, $3}' sample_1.bed > sample_2.bed
• 0 views • link
written by evafinegan • evafinegan

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