Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?

Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?

0

Hi,

I don’t know much about bioinformatics and R language, I just know how to use some bioinformatic tools in a simple way. That´s why I prefer to follow simple tools to analyze my Illumina seqs as I can.

I wonder if it is suitable to apply QC steps in assembled paired-end fastq files. I´m using cutadapt 3.4 and as you know cutadapt 3.4 supports trimming of paired-end reads with basic command line syntax:

cutadapt -a ADAPTER_FWD -A ADAPTER_REV -o out.1.fastq -p out.2.fastq reads.1.fastq reads.2.fastq

After trimming process, I´m using FastQC tool to check the quality. So, I prefer to work assembled fastq files into one fastq rather than two. But I have some concerns about this step.

Do you have any recommendation or idea about this issue? And if you recommend me to work with two fastq pairs during whole QC step, do you know how I can check these pairs with FastQC?

Thank you so much for your help!


QC


cutadapt


Illumina


trimming


3.4

• 29 views

Read more here: Source link