quality scores using consed/phrap/phred

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quality scores using consed/phrap/phred

Sampson, Joshua (NIH/NCI) [E]
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

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Re: quality scores using consed/phrap/phred

Sven Klages-2
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
> [hidden email]
> http://www.bio.net/biomail/listinfo/autoseq

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Re: quality scores using consed/phrap/phred

Phillip SanMiguel
In reply to this post by Sampson, Joshua (NIH/NCI) [E]
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

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quality scores using phred from MegaBACE esd files

Alejandro Gonzalez-3
In reply to this post by Sven Klages-2
  Hi good morning.

I'm user of MegaBACE 1000 DNA sequencer,  my sequences using
MegaBACE1000pack software v 3.1 runing in Windows XP ServicePck3. The
problem that Ihave an interphace soft (CodonCode corp.) to change score
quality megabace to score phred doesn't run in this operative windows.

-Any suggest about how I have to do with the analyzed .esd files from
MegaBACE 1000 to change to score phred?
-there's another program or software to do this and compatible to run in
Windows XP Srvice pck3?

I can manage and use this .esd files to see sequence and make consensus
analysis, but we need get really phred score in all fragments sequences.

Thnks a lot for any help
regards

Lic. Alex González
Argentina GemaBiotech

El 22/10/2009 13:09, Sven Klages escribió:
> hat 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.

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Re: quality scores using phred from MegaBACE esd files

Sven Klages-2
Hi Good Evening ;-)

[...]
> I can manage and use this .esd files to see sequence and make consensus
> analysis, but we need get really phred score in all fragments sequences.
>

Why don't you use 'phred' to re-basecall the ESD files to finally have
SCF and/or PHD or whatever files?

CodonCode Aligner can handle these file types.

cheers,
Sven

> Thnks a lot for any help
> regards
>
> Lic. Alex González
> Argentina GemaBiotech
>
> El 22/10/2009 13:09, Sven Klages escribió:
>> hat 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.
>
> _______________________________________________
> Autoseq mailing list
> [hidden email]
> http://www.bio.net/biomail/listinfo/autoseq

--
  Sven  Klages
  Max Planck Institute for Molecular Genetics
  Ihnestrasse 63/73,  D-14195 Berlin (Dahlem)

  Fon : +49 (30) 8413 1177
  Fax : +49 (30) 8413 1365
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