This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Convert a bed file to bigbed

I have downloaded a bed file from here https://remap.univ-amu.fr/ for the Arabidopsis genome. I want to add the bed file as a custom track to my Arabidopsis genome, but I fail to convert the bed file to bigBed

You can see all my data in the following link. https://drive.google.com/drive/folders/1-wmbc9gKtbXFJ95E0n41WgPL-G313SNe?usp=sharing

When I use the following command

bedToBigBed -tab remap2022_sorted.bed arath.chrom.sizes remap.bb

I take this error

Error line 874 of remap2022_sorted.bed: Expecting colour to consist of r,g,b values from 0 to 255. Got [153,209,10,43,5,32]

I have two questions:

  1. How can I create an r,g,b column in my bed file? Do you have any software to suggest?
  2. Is there software which converts bed files to bed12 files?

Any hint or direction is highly appreciated.

bed bed12 ucsc
• 2,028 views • link
updated by Matthias Zepper Matthias Zepper • written by LDT • LDT

1 answer

Your approach is correct, but there is an issue with your data.

The UCSC Genome Browser Help describes the bed format in detail and as you can see, some lines are malformed:

1   20850   21254   LFY:seedling    2   .   21025   21026   153,209,10,43,5,32
1   37934   38232   LFY:seedling    2   .   38080   38081   153,209,10,43,5,32

With

sed 's/,/\t/3' remap2022_sorted.bed > remap2022_sorted_split.bed

you can fix that as far as the colours are concerned. But the remainder 43,5,32 doesn't really make sense. (It could be a second colour code that was erroneously concatenated instead of substituted?)

According to the .as file, you should have tree more columns

int blockCount;    "Number of blocks"
int[blockCount] blockSizes; "Comma separated list of block sizes"
int[blockCount] chromStarts; "Start positions relative to chromStart"

and this data doesn't add up. So maybe it is the safest to drop it?

See more details about BigBed creation in this blogpost.

• 0 views • link
written by Matthias Zepper Matthias Zepper

Log in to answer this question.

More posts like this