how to merge pair-end reads with maximum score 41 (J)

Question

[tiantai_wing]

I want to merge my pair-end reads into one single reads with about 50 bp overlap. However, my fastq file is Illumina-1.8 Phred+33 format, so the maximum score is 41 (J). I tried NGmerge for merging but it can not expand to score 41 with -u 41 and editing the qual_profile. Is there any other method available to merge this kind of data? Need your help. Thank you!

[GenoMax]

Have you tried bbmerge.sh from BBMap suite? A guide is available here.

[h.mon]

Any paired-end read merger (FLASH, PEAR, BBMerge, and several others) will merge Illumina-1.8 (Phred+33) fastq files without problems, as this is the current standard Illumina format, and by far the most common enconding found in the databases.

What is the problem you are having? What do you expect when you merge R1 and R2? It seems you expect the score of merged bases will be higher than 41, but this is not happening - is this the problem?

[tiantai_wing]

Thanks all! bbmerge is so fast (merging in 2 min for 7 million paired-reads)!