I am losing a lot of seq after the merging step

Dear team,

I have issue i am losing a lot of sequences after the merging, any suggestions?

Hello Desert,

The strategy here is to trim off more of the low quality ends of the reads so that more pass filter and more are able to join. Check out this thread about finding how much you can trim off.

As a bonus, this should make more of your reads pass the input filter too!

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