Tracks exported as BED files are not necessarily in BED format.

[elmo4...@gmail.com]

Tracks exported as BED files are not necessarily in BED format.

For example, working with Hg19 using IGV 2.3.81 (127), I exported the visible features in the RefSeq genes track.  The output file had the extension .bed, but when it was examined it looked like this:

593    NR_029639    chr1    +    1102483    1102578    1102578    1102578    1    1102483,    1102578,    0    MIR200B    unk    unk    -1,
593    NR_029834    chr1    +    1103242    1103332    1103332    1103332    1    1103242,    1103332,    0    MIR200A    unk    unk    -1,
593    NR_029957    chr1    +    1104384    1104467    1104467    1104467    1    1104384,    1104467,    0    MIR429    unk    unk    -1,

This is not BED format at all, rather it is in the format the UCSC Table Browser generates when the output format is "all fields from selected table". The only difference is that UCSC provides a header describing the columns.

Is this by design?  Would it be possible to give the option of getting true BED output, and/or indicate the format that is being used for any given export?

[Jim Robinson]

Hi,

You are correct that is UCSC table browser format.   In general it exports annotations in the format they were loaded in so that information is not lost (that part is by design),  it is a bug to call that "bed output",  and yes we should indicate by extension or otherwise what the output is.   If possible could you log this request in our git issue forum?  

Jim