From Joshua.Sampson from nih.gov Thu Oct 22 09:09:17 2009 From: Joshua.Sampson from nih.gov (Sampson, Joshua (NIH/NCI) [E]) Date: Thu Oct 22 09:33:11 2009 Subject: [Automated-sequencing] quality scores using consed/phrap/phred Message-ID: <9EF08B4E878EC642ADFB069FAC831256AA8B77ED0B@NIHMLBX03.nih.gov> Let me open with the standard disclaimor that I'm new to these packages and therefore apologize if i'm submitting an obvious question. I have received a set off .SFF files that I would like to process/align. Running consed gives me an .ace file with fragments and their starting points in the reference sequence. This is great. However, I would also like the quality score for every base in every fragment (not just the consensus sequence). If I had chromat files, I could see how to do this with Phred. However, all I have is the .SFF files. Any suggestions on how to get the Phred Quality Scores for the fragements? Any help would be greatly appreciated. Josh From klages from molgen.mpg.de Thu Oct 22 11:09:24 2009 From: klages from molgen.mpg.de (Sven Klages) Date: Thu Oct 22 11:28:55 2009 Subject: [Automated-sequencing] quality scores using consed/phrap/phred In-Reply-To: <9EF08B4E878EC642ADFB069FAC831256AA8B77ED0B@NIHMLBX03.nih.gov> References: <9EF08B4E878EC642ADFB069FAC831256AA8B77ED0B@NIHMLBX03.nih.gov> Message-ID: <4AE083B4.8020503@molgen.mpg.de> Hi Joshua, if you use current consed's add454Reads.perl it's doing everything for you. After opening the ace file you can normally work with your sequences .. Sorry, I don't see the problem!? cheers, Sven +++ Sampson, Joshua (NIH/NCI) [E] (22.10.2009 16:09): > Let me open with the standard disclaimor that I'm new to these packages and therefore apologize if i'm submitting an obvious question. > > I have received a set off .SFF files that I would like to process/align. > > Running consed gives me an .ace file with fragments and their starting points in the reference sequence. This is great. > > However, I would also like the quality score for every base in every fragment (not just the consensus sequence). If I had chromat files, I could see how to do this with Phred. However, all I have is the .SFF files. Any suggestions on how to get the Phred Quality Scores for the fragements? > > Any help would be greatly appreciated. > > Josh > > _______________________________________________ > Autoseq mailing list > Autoseq@net.bio.net > http://www.bio.net/biomail/listinfo/autoseq From pmiguel from purdue.edu Thu Oct 22 11:36:07 2009 From: pmiguel from purdue.edu (Phillip San Miguel) Date: Thu Oct 22 11:36:45 2009 Subject: [Automated-sequencing] Re: quality scores using consed/phrap/phred In-Reply-To: References: Message-ID: <4AE089F7.20201@purdue.edu> Sampson, Joshua (NIH/NCI) [E] wrote: > Let me open with the standard disclaimor that I'm new to these packages and therefore apologize if i'm submitting an obvious question. > > I have received a set off .SFF files that I would like to process/align. > > Running consed gives me an .ace file with fragments and their starting points in the reference sequence. This is great. > > However, I would also like the quality score for every base in every fragment (not just the consensus sequence). If I had chromat files, I could see how to do this with Phred. However, all I have is the .SFF files. Any suggestions on how to get the Phred Quality Scores for the fragements? > > Any help would be greatly appreciated. > > Josh > Hi Joshua, sff files are generated by a Roche 454 sequencer. Fasta and qual info can be extracted from them using sffinfo -- a program Roche provides. Use sffinfo -h to get the documentation. -- Phillip From mgonzalez from proyinves.ulpgc.es Wed Oct 28 11:19:14 2009 From: mgonzalez from proyinves.ulpgc.es (=?iso-8859-1?Q?Miguel_Angel_Gonz=E1lez?=) Date: Wed Oct 28 22:03:59 2009 Subject: [Automated-sequencing] Genotyper and Windows 2000 Message-ID: <000401ca57ea$63f16a50$0698230a@pc001> Dear Lynn Petukhova, I have just see your question about Genotyper software and Windows XP in a web forum. Could you say me how could you run Genotyper in Windows Xp system, please? Thank in advance, Miguel Angel Dr. Miguel Angel Gonz?lez P?rez Departamento de Biolog?a Universidad de Las Palmas de Gran Canaria Campus Universitario de Tafira 35017 Las Palmas de Gran Canaria Canary Islands Spain Phone: (+34) 928 454 543 Fax: (+34) 928 452 922 From pmiguel from purdue.edu Thu Oct 29 06:28:59 2009 From: pmiguel from purdue.edu (Phillip San Miguel) Date: Thu Oct 29 06:30:23 2009 Subject: [Automated-sequencing] Re: Genotyper and Windows 2000 In-Reply-To: References: Message-ID: <4AE97C7B.5010400@purdue.edu> Miguel Angel Gonz?lez wrote: > Dear Lynn Petukhova, > > I have just see your question about Genotyper software and Windows XP in a > web forum. Could you say me how could you run Genotyper in Windows Xp > system, please? > > > Thank in advance, > > Miguel Angel Hi Miguel, I don't know whether Lynn Petukhova still follows this forum after her 2002 response to a post "Genotyper and Windows 2000". If no one here has run Genotyper under XP, maybe someone on the ABRF forum will have. Some things you might try: if you run on Vista, you can right-click and run an application as if it were running on an earlier version of the operating system. I doubt that will work, but might be worth a shot. Another possibility is to install a virtual machine running an earlier version of windows on your current machine. I have never done this, but it might be worth a shot. Finally, Applied Biosystems does have a free application "Peak Scanner", that might do at least part of what you wanted to do with Genotyper. Good Luck, -- Phillip