Looking for help joining paired-end reads

[SoilRotifer (Mike Robeson)]

@thermokarst

I think that means there is no way the fwd and rev reads can overlap:

411 nt amplicon |----------------------------------------------|
220 nt fwd read |-------------------->
180 nt rev read                          <---------------------|
11 nt gap                             ^^^

@SoilRotifer, am I doing this math right?

Yeah that works out!

I think your forward reads look great @Hui_Yang! Based on the demux paired-end output, you should be able to go out to further for each read.

Based on the co-ordinates of the demux qzv file, I'd try the following truncation point values (or combinations thereof) :

• FW: 268 | 283
• REV: 211 | 243

I'd try the 268 - 211 pair first.

RE

@Hui_Yang

I got demultiblexed raw data but I couldn’t remove the primers (somehow the tool they provided didn’t work) so I trimmed off 20 nts on the left side of R1 and R2.

Why not try running q2-cutadapt on your demuxed data prior to dada2 / deblur? You can search the forum for many examples of running cutadapt. Then re-visualize your cutadapt output (quality plots) the same way you did your demuxed data. This will help you determine the appropriate truncation points after the primers have been removed, i.e. they'll likely be 20-30 bp shorter. At this point there is likely no need to use the trim options.

-Cheers!
-Mike