changing quality score of the read

Question

[madhu.9124]

Hi,

I want to change the quality score of the read, any suggestions would be appreciated.

Thanks

[Brian Bushnell]

Perhaps you can clarify this? Explaining what kind of data you have, as well as why and how you want to change the quality would be a good start. Also, what you mean by "quality score" (sometimes people mean base quality, and sometimes they mean mapq).

[GenoMax]

Previous questions by OP have been about MAPQ (Obtaining Mapping Quality ( MAPQ) value from samtool ). It is not clear what OP exactly wants to do.

[madhu.9124]

I am basically testing BBmap application, so I am checking whether increase in quality score of the mapped sequence influence the output mapping. I have read and mapped with the reference ecoli read. I want to know increase the quality score of the mapped sequence.

[BioinfGuru]

Can I just ask - how is the quality score increased?

[Brian Bushnell]

Increasing the quality score of reads will lead to an increased mapping rate, because BBMap ignores sequences with really low quality, and does not even try to map reads in which most of the kmers are almost certainly incorrect, according to the quality scores. Thus, you can inflate the mapping rate by assigning Q41 to all bases. The difference will usually be slight, but interesting if you have data with incorrect quality scores. Unfortunately, modern Illumina software does not report correct quality scores. The quality scores from modern Illumina software are garbage and should never be used without recalibration. In fact, I have tested their NovaSeq platform and the quality scores they assign to reads are actually worse than picking numbers at random.

[madhu.9124]

thanks, which tool would you recommend to retrieve quality score and I want to manipulate the score as well.

[BioinfGuru]

"The quality scores from modern Illumina software are garbage" - do you have any review paper that looks into this?

found it - NovaSeq quality analysis