Obtain phred scores for each read

Question

[anuradharavi10]

Hello,

I have some nanopore reads that have a complex insertion. I would like to extract the phred quality scores for each base within the read to assess the quality of the insertion sequence. I have only found tools that can obtain the mean quality scores for reads. however I would like to have individual quality score for each read.

Any help is appreciated!

[GenoMax]

I would like to extract the phred quality scores for each base within the read to assess the quality of the insertion sequence

How do you envision this working as a test of quality? When the Q scores are assigned by the basecaller is not going to know or care about the inserted bases.

however I would like to have individual quality score for each read.

This probably needs to say each base? You could convert the encoded Q scores back to the original number.

[dthorbur]

If you map them to a reference genome you can use the resulting bam file in IGV to view the putative insertion.