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@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu Begin forwarded message:
From: Radek Szklarczyk <radek@cs.vu.nl> Date: January 17, 2006 7:05:00 AM EST To: Anton Nekrutenko <anton@bx.psu.edu> Subject: [Fwd: mail failed, returning to sender]
It bounces from galaxy@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@few.vu.nl> To: radek@cs.vu.nl
|------------------------- Failed addresses follow: ---------------------| <galaxy@bx.psu.edu> ... transport smtp: 550 <galaxy@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@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@cs.vu.nl, www.cs.vu.nl/~radek
The wiki page says users should contact galaxy-user@bx.psu.edu, but the center panel of the initial Galaxy screen still says galaxy@bx.psu.edu. Even when this is fixed, some users may remember the old address, have it in their address books, reply to an old message, etc. Can we have galaxy@bx.psu.edu automatically forward to galaxy-user? Bounces from published addresses do not look good... -Cathy On Tue, Jan 17, 2006 at 09:13:29AM -0500, Anton Nekrutenko wrote:
Begin forwarded message:
From: Radek Szklarczyk <radek@cs.vu.nl> Date: January 17, 2006 7:05:00 AM EST To: Anton Nekrutenko <anton@bx.psu.edu> Subject: [Fwd: mail failed, returning to sender]
It bounces from galaxy@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@few.vu.nl> To: radek@cs.vu.nl
|------------------------- Failed addresses follow: ---------------------| <galaxy@bx.psu.edu> ... transport smtp: 550 <galaxy@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@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@cs.vu.nl, www.cs.vu.nl/~radek
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participants (2)
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Anton Nekrutenko -
Cathy Riemer