Wrong (low quality) bases in overlapped regions failed to be corrected

[drna]

AfterQC has helped me to improve the quality of my data. Thanks for creating it.

I did notice, though, that some wrong (low quality) bases in overlapped regions failed to be corrected and I am not sure why.

Could you perhaps have a look, below one read as an example.
---------------- test_R1.fastq
@NS500261:202:HKMTKAFXX:1:21112:5370:11983 1:N:0:ATCTAGCCGGCC
CTGCGCCTGGTTGGGCATCGCTCCGCTAGGTGTCAGCGGCTCCACCAGCTGGGGTGAGGGGGTGGTGGGTCAGTGCTGGGGGCCGGTGCAGACCCCACGCGGGCTGGGAGGACTTCACCCCGCCTCACCTCCGTTTCCTGCAGATCGGAAG
+
AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEAEEEEEEEEEEEEEEEEEE/EEEE/EEEEEEEEEEEAEE/AA<AAEEAAAAAEE<EAAA<A<6AAAAE<<AEAAAAAEE
---------------- test_R2.fastq
@NS500261:202:HKMTKAFXX:1:21112:5370:11983 2:N:0:ATCTAGCCGGCC
GCAGGAAACGGAGGTGAGGCGGGGTGAAGTCCTCCCAGCCCGCGTGGGGTCTGCACCGGCCCCCAGCCCTGACCCACCACCCCCTCACCCCAGCTGGTGGAGCCGCGGCCCCCTAGCGGCGCGATGCCCAACCAGGCGCAGAGCTC
+
AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAEEEEEEE/AE/E/E/EEE/EE/EEEEE/EAE6EE/EE//E/E//EEE/A/A/E/AE/AAE/E/EE</<AAEE//AE//<E6E////6<<

[sfchen]

This pair of reads have too many mismatches (5 in total).

AfterQC will skip correcting the overlaps with mismatches > 3. This is to avoid over-correction.

[drna]

It makes sense! Can the threshold be adjusted?

[sfchen]

I will update AfterQC to make it adjustable.

[drna]

Fantastic! Thanks