Dear all,

My goal is to upload a new Genome as a track Hub in the UCSC genome browser.

I have followed the tutorial here and here in detail. I am trying to convert my bed file to bigBed, and I keep getting an error that this is not a .bigBed file. I share my data at the address.

I am using the new _Arabidopsis thaliana_ as a test genome for uploading in the UCSC browser. I have downloaded the kent Utilities as it is indicated in the tutorials.

First I am converting the gff3 file of _Arabidopsis thaliana_ to a bed file, using agat

agat_convert_sp_gff2bed.pl -gff Arabidopsis_thaliana_TAIR10.gff3 -o arath_gff.bed

Then i sort the bed file

sort -k1,1 -k2,2n arath_gff.bed > arath_gff_sorted.bed

Lastly, I have used different commands to convert .bed to .bigBed but none really works.

bedToBigBed arath_gff_sorted.bed arath.chrom.sizes arath.bigBed

or

bedToBigBed -type=bed12+ -as=bed12Source.as -tab arath_gff_sorted.bed arath.chrom.sizes arath.bigBed

To evaluate if my .bigBed file is functional, I am using the following command

bigBedToBed -chrom=chr1 -start=1 -end=10 arath.bigBed stdout

Which gives me the following error: arath.bigBed is not a big bed file

any help or guidance are appreciated!