Convert .gff3 file to 12-column .bed file

[SuzuBell]

Hello:

I would like to convert .gff3 file to 12-column .bed file, as in this link under "BED Format" (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).

I have thusfar used Galaxy from Penn State, but it outputs a 6-column .bed file.

Any advice is greatly appreciated! Thank you...

[daniel_g]

It depends on the complexity of your task, but if all you want to do is remove or rearrange columns (e.g. changing a 6-column bed to a 4-column bed) I usually find awk to be the quickest tool.

A short tutorial: http://www.hcs.harvard.edu/~dholland/computers/awk.html

[SuzuBell]

Daniel:

Thank you, I did try to do that(simply rearrange columns), but am still uncertain for how to create certain columns of the .bed file. I think I can create Columns 1 2, 3, 5, 6, 7, 8: Bed(Col1) = Gff3 (Col1)
Bed(Col2) = Gff3(Col4)
Bed(Col3) = Gff3(Col5)
Bed(Col5) = Gff3(Col6)
Bed(Col6) = Gff3(Col7)
Bed(Col7) = Bed(Col2) [at least in online examples, it seemed repeated]
Bed(Col8) = Bed(Col3) [at least in online examples, it seemed repeated]

But then, I am left with Columns 4, 9, 10, 11, 12. For Col 4, I don't know how to get the "name" from the Gff3 file. For Col 9, I don't know how to get the "itemRGB" from the Gff3 file. For Col 10, I am not sure what the "BlockCount" is. At first, I thought there could only be 0 or 1 exons on the line, and so this column could either be "0" or "1". But that would not make sense for Col 11 and Col 12, because these require comma-separated lists for each element in the blockCount (meaning, I assume, Col 10 has the potential to be >1).

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Just in case, here is a head of my .gff3 file:

PdomScaf0001 maker gene 15 1963 . - . Name=PdomGene00025;ID=1;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274

PdomScaf0001 maker mRNA 15 1963 . - . Name=PdomMRNA00025.1;Parent=1;ID=2;_QI=216%7C0%7C0.2%7C0.6%7C0.5%7C0.6%7C5%7C0%7C98;_eAED=0.43;_AED=0.43;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274-mRNA-1

PdomScaf0001 maker exon 15 100 -0.094 - . Parent=2;ID=3

PdomScaf0001 maker CDS 15 100 . - 2 Parent=2;ID=4

PdomScaf0001 maker exon 223 300 21.8 - . Parent=2;ID=5

PdomScaf0001 maker CDS 223 300 . - 2 Parent=2;ID=6

PdomScaf0001 maker exon 717 765 22.4 - . Parent=2;ID=7

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And a head of my .bed file, created using gff2bed (same as you suggested):

PdomScaf0001 14 100 3 -0.094 - maker exon . Parent=2;ID=3

PdomScaf0001 14 100 4 . - maker CDS 2 Parent=2;ID=4

PdomScaf0001 14 1963 1 . - maker gene . Name=PdomGene00025;ID=1;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274

PdomScaf0001 14 1963 2 . - maker mRNA . Name=PdomMRNA00025.1;Parent=1;ID=2;_QI=216%7C0%7C0.2%7C0.6%7C0.5%7C0.6%7C5%7C0%7C98;_eAED=0.43;_AED=0.43;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274-mRNA-1

PdomScaf0001 222 300 5 21.8 - maker exon . Parent=2;ID=5

PdomScaf0001 222 300 6 . - maker CDS 2 Parent=2;ID=6

PdomScaf0001 716 765 7 22.4 - maker exon . Parent=2;ID=7

PdomScaf0001 716 765 8 . - maker CDS 0 Parent=2;ID=8

PdomScaf0001 906 947 9 4.85 - maker exon . Parent=2;ID=9

PdomScaf0001 906 947 10 . - maker CDS 2 Parent=2;ID=10