Cut adapt for Single end Sequences

[SoilRotifer (Mike Robeson)]

Hi @Ankush_1,

If you search the forum you'll see that others have come across this issue. The secret is:

q2-cutadapt output

The likely reason you are loosing so many reads is due to excessive mismatches as a result of IUPAC ambiguity codes in your primers. Try adding the --p-match-adapter-wildcards flag. More information can be found here:

There are other good suggestions in that thread too.

Also, you'll likely only need to enter in the forward primer, i.e. --p-front, often you'll not need to enter in the adapter sequence unless you expect read-through.

-Cheers!
-Mike