Overlapping regions in a BED file
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6 weeks ago
Matej • 0

I was looking at a simple visualization program that, among other things, visualized BED file with respect to the inputted FASTA ref sequence. I noticed that there were separate tracks for annotations and that there very many regions that were overlapping. I'm having a hard time understanding that, can someone explain to me how can coding regions overlap in a BED file?

edit: Since I see that I created somewhat of a confusion with my not-so-clear question, basically I'm asking if someone can explain to me how is it possible that coding regions overlap in a BED file.

For example, these are couple of lines from my Escherichia_coli_id52271.bed file:

1    5262    5712    E4287_5.mRNA1    449    +    .    .    .    1    450    0    mRNA
1    5262    5712    E4287_5    449    +    .    .    .    1    450    0    gen
...
1    6729    7644    E4287_7    914    +    .    .    .    1    915    0    gene
1    6729    7644    b0030    914    +    .    .    .    1    915    0    CDS
regions BED Sequence exons annotation • 891 views
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There are many (unrelated) questions here without context (what is "separate tracks for annotation" ? "how can coding regions overlap in a BED file" ? ).

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Okay yeah, maybe I wasn't focused enough in my question, my main question is how can coding regions overlap in a BED file

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multiple transcripts, interleaved genes: the question is why wouldn't they overlap ? please, show us and example.

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I've edited my question with couple of examples. In the examples provided, the regions don't just overlap, they are exactly the same and I'm having a hard time understanding that.

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1    5262    5712    E4287_5.mRNA1    449    +    .    .    .    1    450    0    mRNA
1    5262    5712    E4287_5    449    +    .    .    .    1    450    0    gen

what's the definition of this BED file ? I see a coordinate for a mRNA coded by a gene. As it' in a bacteria, of course, it 's the very same coordinate.

Your file looks like a modified GTF file.

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What do you mean by definition?

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what's the meaning of the columns 'mRNA' and 'gen' ?

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I'm not sure, I downloaded the bed file from here. I also found it weird that it had this extra column but I didn't know what to make of it.

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Maybe answer doesn't have to be specific to this file, what is a simple explanation why would two lines in BED file have the same coordinates, or why would they overlap ?

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why would two lines in BED file have the same coordinates, or why would they overlap ?

again , if one line is for mRNA, and the other is for gene, it's normal.

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What does that mean exactly? Sorry for bothering you this much

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They are standard feature types (describing gene and its products) that are defined in GTF/GFF files from which your BED file is likely derived from: https://www.ncbi.nlm.nih.gov/genbank/genomes_gff/#attributes and http://gmod.org/wiki/GFF2#Using_the_Group_field_for_simple_features

Gene: https://en.wikipedia.org/wiki/Gene#Structure_and_function

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Okay, thank you very much, but besides this being a BED file derived from GTF/GFF, what else could be a reason for overlapping features ?

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what else could be a reason for overlapping features ?

In a word, Biology. mRNA is a product produced from a gene. In case of bacteria sizes for these two may be equivalent since there is no splicing (exon/introns).

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But also a gene can have multiple transcriptions, correct ?

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