bioinformatics

Marcela Uliano · 04-10-2012, 08:41 PM

Hey guys!

I was wondering how should I interpret the quality scores coming from results from 454 GS jr cDNA (not paired end) reads?

I mean, I read a lot that its prhed-like. But as the sequencing techniques from sanger and pyrosequencing are so different from each other, I wonder if its true.

Could you help me find literature about these quality scores thing and to be able to understand by analyzing my data if the quality of my reads are good or not?

Im a little confuse about that and havent got to any conclusions so far.

Thanks a lot!

maubp · 04-11-2012, 03:57 AM

Well they are using the same PHRED logarithmic scoring scale (probability of error), but given the typical error in Roche 454 reads is in homopolymer repeat number this doesn't map well to a per-base quality score.

Marcela Uliano · 04-11-2012, 06:40 AM

Thanks maubp

So the quality valeu coming with the sff file or the one from the fasta format (fna), the .qual are based on PHRED logarithmic scale?

maubp · 04-11-2012, 06:43 AM

The SFF file contains the called bases (which can be turned into a FASTA file) and the associated per-base PHRED quality scores (which can be turned into a QUAL file).

It might help to change the title of your thread from 'Bioinformatics' to something like 'Interpreting Roche 454 per-base quality scores'.

Marcela Uliano · 04-11-2012, 07:08 AM

Thanks a lot maubp!

Ill do that. But you, pretty much, have already helped me to solve my doubt!

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04-10-2012, 08:41 PM	#1
Marcela Uliano Member Location: Berlin, Germany Join Date: Apr 2012 Posts: 18	bioinformatics Hey guys! I was wondering how should I interpret the quality scores coming from results from 454 GS jr cDNA (not paired end) reads? I mean, I read a lot that its prhed-like. But as the sequencing techniques from sanger and pyrosequencing are so different from each other, I wonder if its true. Could you help me find literature about these quality scores thing and to be able to understand by analyzing my data if the quality of my reads are good or not? Im a little confuse about that and havent got to any conclusions so far. Thanks a lot!

04-11-2012, 03:57 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Well they are using the same PHRED logarithmic scoring scale (probability of error), but given the typical error in Roche 454 reads is in homopolymer repeat number this doesn't map well to a per-base quality score.

04-11-2012, 06:40 AM	#3
Marcela Uliano Member Location: Berlin, Germany Join Date: Apr 2012 Posts: 18	Thanks maubp So the quality valeu coming with the sff file or the one from the fasta format (fna), the .qual are based on PHRED logarithmic scale?

04-11-2012, 06:43 AM	#4
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	The SFF file contains the called bases (which can be turned into a FASTA file) and the associated per-base PHRED quality scores (which can be turned into a QUAL file). It might help to change the title of your thread from 'Bioinformatics' to something like 'Interpreting Roche 454 per-base quality scores'.

04-11-2012, 07:08 AM	#5
Marcela Uliano Member Location: Berlin, Germany Join Date: Apr 2012 Posts: 18	Thanks a lot maubp! Ill do that. But you, pretty much, have already helped me to solve my doubt!