After getting a relatively high percentage of undetected guides in our control condition, the NGS facility recommended merging overlapping paired-end NSG reads to improve the 'quality' of our data. Does anyone have experience merging paired-end reads? Any tools to merge that you'd recommend? Any help would be greatly appreciated!
I recommend using the FastqGeneralIterator from Biopython. See example here.
How high was your percentage of undetected guides? Did a lot of your NGS reads have the key? Generally merging the paired-end reads should not be necessary (we only sequence read 1 when we QC our libraries). A lot of times people used the wrong "-g" flag for the library, leading to a high percentage of key detection, but low guide detection.