Question: bedtools not working with gff from flybase
0
gravatar for asif.zubair
3.1 years ago by
United States
asif.zubair0 wrote:

Hi,

I got a gff file from flybase that i am trying to use with bedtools. However, it is throwing an error:

(0)> bedtools intersect -a my.vcf -b dmel-2L-r5.41.gff
Error: Invalid record in file dmel-2L-r5.41.gff. Record is 
2L      FlyBase chromosome_band -204333 1326937 .       +       .       ID=band-21_chromosome_band;Name=band-21

I downloaded the gff from here

I don't know why this format would be incorrect. From what I know of gff files, it seems correct.

Any help would be appreciated.

Thank you,
Best,

asif

flybase gff vcf bedtools • 934 views
ADD COMMENTlink written 3.1 years ago by asif.zubair0
1

Why's your start coordinate negative?

ADD REPLYlink written 3.1 years ago by Sam2.3k
1
gravatar for asif.zubair
3.1 years ago by
United States
asif.zubair0 wrote:

Yes, it turns out there is a problem with flybase's gff file. It seems flybase people fixed that in a newer version.

Thank you for pointing it out!

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by asif.zubair0
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