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Old 04-15-2011, 07:39 AM   #1
andreitudor
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Default 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.
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Old 04-15-2011, 01:26 PM   #2
westerman
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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.
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Old 04-15-2011, 01:27 PM   #3
n00c
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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
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Old 04-15-2011, 05:25 PM   #4
andreitudor
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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.
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Old 04-18-2011, 08:51 AM   #5
westerman
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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/
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Old 04-18-2011, 01:43 PM   #6
JackieBadger
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Quote:
Originally Posted by westerman View Post
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/
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Old 04-18-2011, 01:46 PM   #7
JackieBadger
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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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