Merging forward and reverse casava one eight

[Fra (Francesco)]

Hello everybody,

few weeks ago I posted a topic asking how to import my sequences. Someone replied saying my sequences were “casava” and following this advice I successfully import my raw reads in QIIME.

Afterward, I realised that going through the pipeline there wasn’t a command to merge my forward and reverse reads.

Due to the fact I would prefer to analyse my combined reads rather than only the forwards, does anyone can suggest me a solution?

Here a subsample of my raw dataset:

A7-S501-N706_S41_L001_R1_001.fastq.gz
D8-S504-N705_S36_L001_R1_001.fastq.gz
G7-S507-N706_S47_L001_R1_001.fastq.gz
A7-S501-N706_S41_L001_R2_001.fastq.gz
D8-S504-N705_S36_L001_R2_001.fastq.gz
G7-S507-N706_S47_L001_R2_001.fastq.gz

Cheers
Fra

[Nicholas_Bokulich]

@Fra,

@Fra

Afterward, I realised that going through the pipeline there wasn’t a command to merge my forward and reverse reads.

Have you had a chance to read through the QIIME2 tutorials? There are many examples for how to perform read joining of paired-end reads. For example, dada2 can do this as part of the denoise-paired method, as detailed in the atacama soils tutorial. If you want to use deblur or otu picking instead, see the read joining tutorial.

Good luck!