Most reads failed to merge due to staggered read pairs

[colinbrislawn (Colin J Brislawn)]

@amirza

You meant --p-allowmergestagger flag correct?

That's right. Good catch!

I'm glad you got more of your reads to pair.

@amirza

Is it worth trimming off the at the ends (before merging) to increase the quality of the reads but sacrificing sequence overlap?

Yes, that's a great idea.

Also, the default --p-maxdiffs 10 is super low. I would up that to at least 20 (or 30!!) and see if your reads get paired.

The alignment score too low is harder to fix. Some reads just don't pair.

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@amirza

I was surprised that this became an issue because im sure many are also using the V4 region and have used cutadapt without the --p-allowmergestagger flag but have not reported any problems. Why was this only an issue for me?

I'm not sure either. This is good question to bring up with your sequencing provider or PI. Are these the EMP primers or from another organization? That could explain differences in region sequenced, and thus in pairing.

Colin