Hi Jeremy,

Things do indeed look much better after your commit last night, thanks:
https://bitbucket.org/galaxy/galaxy-central/changeset/3c7416baa157

On Mon, Aug 15, 2011 at 12:52 AM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
>> Well, sort of. After converting that GFF3 file into BED, the strand column
>> isn't set in the metadata. That seems important!
>
> We'll look into this.

Thanks. If I manually set the BED strand to column 5, then the extract tool
can be used with both the original NCBI GFF3 file and the BED conversion.
I have filtered these on gene features, and noticed a discrepancy.

GFF uses one based numbering, e.g. the gene NEQ003 is 883 to 2691.

For BED the start coordinate is zero-indexed and the end coordinate is
one-indexed (just like Python slicing), thus the gene NEQ003 is 882 to
2691 (and Galaxy converts this correctly).

Using the extract tool with the gene features correctly get the nucleotide
sequence of NEQ003 running from ATG...TAA regardless of if I use the
genes in GFF3 format or in BED format (good).

However, the FASTA output uses different names because it embeds
the start/end co-ordindates as is. Thus using GFF3 features, the
sequence name includes _883_2691_ while using BED features the
same sequence has instead _882_2691_ for its name.

I propose this be harmonised by always using one-based counting
in the FASTA names (as done in GFF files but also GenBank, EMBL,
etc) rather than the convention used in BED files (and Python) which
is confusing to most non-programmers.

Peter
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