Anton Nekrutenko
Assistant Professor
Department of Biochemistry and Molecular Biology
Center for Comparative Genomics and Bioinformatics
505 Wartik Building
PennState University
University Park, PA 16802
814 865-4752
814 863-6699 FAX
anton(a)bx.psu.edu
http://www.bx.psu.edu/~antonhttp://g2.bx.psu.edu
Begin forwarded message:
> From: Radek Szklarczyk <radek(a)cs.vu.nl>
> Date: January 17, 2006 7:05:00 AM EST
> To: Anton Nekrutenko <anton(a)bx.psu.edu>
> Subject: [Fwd: mail failed, returning to sender]
>
> It bounces from galaxy(a)bx.psu.edu (email from the galaxy web site).
> Anyway, I'd like to submit a bug report
> r
>
> -------- Original Message --------
> Subject: mail failed, returning to sender
> Date: Tue, 17 Jan 2006 12:02 +0100
> From: <MAILER-DAEMON(a)few.vu.nl>
> To: radek(a)cs.vu.nl
>
>
>
> |------------------------- Failed addresses follow:
> ---------------------|
> <galaxy(a)bx.psu.edu> ... transport smtp: 550 <galaxy(a)bx.psu.edu>:
> Recipient address rejected: User unknown in local recipient table
> |------------------------- Message text follows:
> ------------------------|
> Received: from [130.37.31.65] (poederdoos.cs.vu.nl [130.37.31.65])
> by top.few.vu.nl with esmtp (Smail #108)
> id m1Eyobm-0002XpC; Tue, 17 Jan 2006 12:02 +0100
> To: galaxy(a)bx.psu.edu
> Subject: bug: genome intervals coord/documentation?
>
> in the help of "file upload" it says that the coords in genomic
> interval file are 0-based, end exclusive. Neither of these seem to
> be true, file:
>
> #CHROM START END STRAND
> chr1 108333207 108333209 +
>
> Extracts the sequence
>
>> hg15_chr1_108333207_108333209_+
> ATG
>
> which is not 0-based (the same seq you can retrieve with genome
> browser, which is 1-based), neither end-exclusive (3 nucleotides).
>
>
> --
> Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek
>
