parameters going into quality scores fastq Illumina
Hi, I would like to understand which parameters, ideally which algorithm go into the scores one obtains from the quality statistics out of fastQ illumina data. What is this score composed of? And how come that applying fastq groomer and then using fastq summary statistics tool gives a different score as using the fast q qc from babraham. I heard fastq groomer may change the data? EXAMPLE: In my example the scores using fastq groomer and then fastq summary statistics were between 3 and 11, whereas using fastq qc straight on the data the score was between 32 and 41. Thank you so much for your explanation. Best regards, CG
On Mon, May 14, 2012 at 9:03 PM, Claudia Gottstein <gottstein@cnsi.ucsb.edu> wrote:
Hi, I would like to understand which parameters, ideally which algorithm go into the scores one obtains from the quality statistics out of fastQ illumina data. What is this score composed of? And how come that applying fastq groomer and then using fastq summary statistics tool gives a different score as using the fast q qc from babraham. I heard fastq groomer may change the data?
EXAMPLE: In my example the scores using fastq groomer and then fastq summary statistics were between 3 and 11, whereas using fastq qc straight on the data the score was between 32 and 41.
Thank you so much for your explanation. Best regards, CG
The Galaxy FASTQ groomer shouldn't change the scores, but it may change the encoding. Did you read the paper cited in the tool's help text? http://dx.doi.org/10.1093/nar/gkp1137 See also http://en.wikipedia.org/wiki/FASTQ_format Peter
participants (2)
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Claudia Gottstein -
Peter Cock