How do i salvage these sequences?

[Adrian_Muwonge]

Hello all, how do i salvage these sequences to run a reasonably descent analysis in QIIME2. See the import file and dada2 output.

As you can see, the first 38 bp did not sequence well, so trimming at 38 -175 the dada output attached is not good at all as you can see very few features are generated per sample.

Any ideas on how i could salvage this?

Thanks in advance

A

[jwdebelius (Justine Debelius)]

HI @Adrian_Muwonge,

First, Im just generally concerned about your sequencing quality. You may want to consider resequencing, since you have very low quality reads forward and reverse. Im glad you trimmed, that’s a good first step. But, did you run DADA2 with paired end sequencing, or only forward reads?

Best,
Justine

[Adrian_Muwonge]

Hello Justine, i wanted to see what could be salvaged as resequencing is going to be an extra cost.
I run DADA2 with with paired end reads, are you suggesting i should trying running with forward reads only?

Adrian

[jwdebelius (Justine Debelius)]

@Adrian_Muwonge,

Yes, you should run DADA2 with forward reads only, because after trimming, you likely don’t have enough high quality sequences to do paired end joining.

Best,
Justine

[Adrian_Muwonge]

Hello Justine, i will give that a try

Adrian

[Adrian_Muwonge]

Thanks Justin, that did the trick

Adrian