NGS reads quality

andreitudor · 04-15-2011, 07:39 AM

Is there a way to find a quality score for a 454 sequence?
I know I have the fasta and qual files, but can I get like a number for every read or all the reads together?

Andrei

EDIT: By reads I mean the raw 454 data.

westerman · 04-15-2011, 01:26 PM

In the D*fullProcessing directory after running Newbler should be *.454Reads.fna and *454Reads.qual files of the reads. Depending on your sequencing facility they may not be giving out those files unless requested. We do not give them out by default since most of our customers are not interested in the data nor (dare I say it?) capable of handling the data.

n00c · 04-15-2011, 01:27 PM

Sounds like you want to convert FASTA+QUAL to FASTQ. BioPython and BioPerl supposedly do this:

http://biopython.org/DIST/docs/tutor...l.html#htoc218
http://www.bioperl.org/wiki/Merging_...files_to_FASTQ

andreitudor · 04-15-2011, 05:25 PM

Yes indeed, I have those files. I have the .sff file, so I have the multi-fasta of the reads, .qual for the reads, and an assembly with newbler. in the newbler assembly directory i have the fasta and qual files of the contigs. I was intrested, and still am, in finding as much info on the reads as possible (quality metrics)

westerman · 04-18-2011, 08:51 AM

Sorry. I missed in your original post that you already had the quality files. Thus my advice was not apropos to your needs.

Basically what you are looking for is a quality metrics program. Doesn't matter if this program is for 454 data or for other sequencers. For such a large number of reads a graphical presentation is the only way to go. The fastqc program from babraham is a good program. Cross-platform.

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

JackieBadger · 04-18-2011, 01:43 PM

Quote:

Originally Posted by westerman

Sorry. I missed in your original post that you already had the quality files. Thus my advice was not apropos to your needs.

Basically what you are looking for is a quality metrics program. Doesn't matter if this program is for 454 data or for other sequencers. For such a large number of reads a graphical presentation is the only way to go. The fastqc program from babraham is a good program. Cross-platform.

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

Hi,

FastQC was not designed for 454 data, and has not been tested on it, so the quality distributions may be misleading.

PRINSEQ, was however designed for 454 data, and is excellent. Even the standalone, Linux platform is very easy to use: http://edwards.sdsu.edu/prinseq_beta/

JackieBadger · 04-18-2011, 01:46 PM

GALAXY can also give you a nice boxplot, but isnt so good for filtering 454 amplicon as the criteria is much stricter... http://main.g2.bx.psu.edu/

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04-15-2011, 07:39 AM	#1
andreitudor Member Location: Quebec Join Date: Feb 2011 Posts: 21	NGS reads quality Is there a way to find a quality score for a 454 sequence? I know I have the fasta and qual files, but can I get like a number for every read or all the reads together? Andrei EDIT: By reads I mean the raw 454 data. Last edited by andreitudor; 04-15-2011 at 07:43 AM.

04-15-2011, 05:25 PM	#4
andreitudor Member Location: Quebec Join Date: Feb 2011 Posts: 21	Yes indeed, I have those files. I have the .sff file, so I have the multi-fasta of the reads, .qual for the reads, and an assembly with newbler. in the newbler assembly directory i have the fasta and qual files of the contigs. I was intrested, and still am, in finding as much info on the reads as possible (quality metrics) Last edited by andreitudor; 04-15-2011 at 05:27 PM.

04-15-2011, 01:26 PM	#2
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	In the DfullProcessing directory after running Newbler should be .454Reads.fna and *454Reads.qual files of the reads. Depending on your sequencing facility they may not be giving out those files unless requested. We do not give them out by default since most of our customers are not interested in the data nor (dare I say it?) capable of handling the data.

04-15-2011, 01:27 PM	#3
n00c Member Location: Boston, MA Join Date: Nov 2009 Posts: 12	Sounds like you want to convert FASTA+QUAL to FASTQ. BioPython and BioPerl supposedly do this: http://biopython.org/DIST/docs/tutor...l.html#htoc218 http://www.bioperl.org/wiki/Merging_...files_to_FASTQ

04-18-2011, 08:51 AM	#5
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	Sorry. I missed in your original post that you already had the quality files. Thus my advice was not apropos to your needs. Basically what you are looking for is a quality metrics program. Doesn't matter if this program is for 454 data or for other sequencers. For such a large number of reads a graphical presentation is the only way to go. The fastqc program from babraham is a good program. Cross-platform. http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

04-18-2011, 01:46 PM	#7
JackieBadger Senior Member Location: Halifax, Nova Scotia Join Date: Mar 2009 Posts: 381	GALAXY can also give you a nice boxplot, but isnt so good for filtering 454 amplicon as the criteria is much stricter... http://main.g2.bx.psu.edu/