Question

rtacklayer::import.bed silently adds 1 to the start coordinates

0

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Mikhail Dozmorov ▴ 30

@mikhail-dozmorov-23744

Last seen 6 weeks ago

United States

When importing a BED file like:

 1 chr1         0   257700
 2 chr1   1125300  1182900

rtracklayer::import.bed() creates a GRanges object like:

             start       end     width
         <integer> <integer> <integer>
     [1]         1    257700    257700
     [2]   1125301   1182900     57600

Is this expected?

It may be something fundamentally basic but I couldn't find an answer. The starts.in.df.are.0based argument in makeGRangesFromDataFrame() is not recognized by rtracklayer::import.bed().

rtracklayer • 1.2k views

ADD COMMENT • link updated 2.3 years ago by ATpoint ★ 4.6k • written 2.3 years ago by Mikhail Dozmorov ▴ 30

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Pretty much the same was asked at biostars the other day: https://www.biostars.org/p/9537845/#9537847

See also this "cheat sheet" towards 0- and 1-based formats: https://www.biostars.org/p/84686/

Actually, everything is 1-based that is human-readable, except BED. Some binary formats are 1-based as well but parsers will handle that internally if you use standard tools such as samtools (BAM for example is 1-based).

ADD REPLY • link 2.3 years ago ATpoint ★ 4.6k

score 0 · Answer 1 · 2022-09-13

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 1 day ago

United States

It is expected. BED format is 0-based, half open, and all of Bioconductor uses 1-based, fully closed.