Error while converting a bed to bigBed file

Question

[LDT]

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!

Answer 1

[seidel]

It's because you have 5692 lines where Field 7 and 8 (thickStart, thickEnd) are "." instead of a number. If you remove these lines, or fix them so they are numeric, you'll get a bigBed file.

[LDT]

Thank you seidel. I removed the rows with ". ", but I still can not make it a bigBed file. Its a pitty because I have reached an edge. Trying over a week

[seidel]

Is your modified file at the address above? If so I will take a look at it.

[LDT]

Dear seidel,

That was a generous move from your side. I appreciate so much. I just found out that there was another mistake at the bed12Source.as. I solved that, and I have a healthy .bigBed file now. However, when I try to do a hubCheck hub.txt in my file, I get an odd error, and it looks like this

Couldn't open arath/trackDb.txt

My data is here https://drive.google.com/drive/folders/1Tc6KzQqmYQ8J3aN2uaY2Og8Dv3zSxx1f, and I have a post about it error: Couldn't open trackDb.txt in hubCheck