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lpantano / seqcluster

small RNA analysis from NGS data
http://seqcluster.readthedocs.io
MIT License
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Regarding of fastq quality by collapse #17

Closed hmkim closed 6 years ago

hmkim commented 8 years ago

Hi, Ipantano

I wonder about the quality score in fastq by collapse

Methods

The new quality values are the average of each of the sequence collapse.

I think preserving the highest average quality score from fastq file is worth more than average for mapping.

lpantano commented 8 years ago

Hi,

in this case is doing the average quality.

I don’t know if your question is related to something else. Then this quality will be used by the mapper, in case it can do it. Then, this will affect the MAPQ in the bam file and other tools can use this to detect SNPs, or related questions.

hope this help.

On Jun 16, 2016, at 11:46 AM, Hyunmin Kim (Brandon) notifications@github.com wrote:

Hi, Ipantano

I wonder about the quality score in fastq by collapse

Methods

The new quality values are the average of each of the sequence collapse.

Is preserving the highest average quality score worth more than averge for mapping?

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hmkim commented 8 years ago

In mapper, MAPQ affected by FASTQ quality score as you said.

When the read have the highest quality score, the read's MAPQ will have higher than with average quality score, right?