Separating pooled PCR products after demultiplexing has been done

[Aimee]

Hi there

I am wanting to separate pooled PCR products (paired-end) by their differing primer sequences, which have been demultiplexed.

I initially tried cutadapt, which was great until I realized that the output file was containing all the sequences - trimmed and untrimmed. So, I have tried various ways to remove the unwanted sequences to no avail using Qiime 2 - yet.

My code at the moment:

qiime cutadapt trim-paired
--i-demultiplexed-sequences demux.qza
--p-front-f AGGGCAAKYCTGGTGCCAGC
--p-front-r GRCGGTATCTRATCGYCTT
--p-no-indels
--p-error-rate 0
*--o-discard-untrimmed *
--o-trimmed-sequences trimmed-demux.qza
--verbose

The error I am getting is:

Error: no such option: --p-discard-untrimmed
*same message if I change it to --o

I feel like I am missing something, as this is a filtering option. I previously did this step in Qiime 1, but would like the entire pipeline to now be in Qiime 2. Is this possible?

Many thanks
Aimee

[thermokarst]

Hi @Aimee!

@Aimee

I feel like I am missing something

The docs are always a good place to start!

@Aimee

–o-discard-untrimmed

Unfortunately, we haven't exposed this option in q2-cutadapt due to a technical issue. In the meantime, you can always export from QIIME 2 and run cutadapt directly, using your QIIME 2 environment. Sorry!

[Aimee]

Hi @thermokarst

Thanks for the quick response!

Think I was consulting too many docs at once and got confused, thanks for clarifying.

I did miss this in my q2-cutadapt searching though - so thanks for pointing it out:

we haven’t exposed this option in q2-cutadapt due to a technical issue