Question: How to trim both pair end reads and remove low quality reads
1
gravatar for Bioinfonext
9 months ago by
Bioinfonext160
Korea
Bioinfonext160 wrote:

I do have pair end amplicon data but it looks like data is very poor quality. I want to trim these reads from both end 10bp and also want to remove low quality reads both R1 and R2. so that at the end no. of pair reads should be same in both files.

currently, I used fastx trimmer and fastx quality filter, but they only take one read file R1 or R2 at a time.

How I can give both file as input for trim and quality filter so that at end R1 and R1 contain high quality reads pair.

I want to trim 10bp from both ends.

Pair end reads path: /users/amplicon_data/ITS

multiple pair end read file name:

Soil-6_S22_L001_R1_001.fastq

Soil-6_S22_L001_R2_001.fastq

Soil-7_S32_L001_R1_001.fastq

Soil-7_S32_L001_R2_001.fastq

Soil-8_S32_L001_R1_001.fastq

Soil-8_S32_L001_R2_001.fastq

Soil-9_S42_L001_R1_001.fastq

Soil-9_S42_L001_R2_001.fastq

thanks

next-gen • 440 views
ADD COMMENTlink modified 6 months ago by SaltedPork100 • written 9 months ago by Bioinfonext160
1

Fastx is very old and not designed to properly handle paired-end data. Recent alternatives skewer, trimmomatic, fastp, cutadapt, bbduk and many more. Please use the search function for more threads

ADD REPLYlink written 9 months ago by ATpoint24k

Trim Galore! is another option, which can run Cutadapt and FastQC at the same time / concurrently.

ADD REPLYlink written 9 months ago by Kevin Blighe49k

And how poor is "very poor"?

ADD REPLYlink written 9 months ago by finswimmer12k
0
gravatar for SaltedPork
6 months ago by
SaltedPork100
SaltedPork100 wrote:

I use Trimmomatic frequently, it's pretty easy to use. Look at the manual, the default options are a good place to start

example command:

java -jar /home/folder.../Trimmomatic-0.38/trimmomatic-0.38.jar PE -threads 4 $Reads1 $Reads2 $sample.hq.1.fastq $sample.unpaired.1.fastq $sample.hq.2.fastq $sample.unpaired.2.fastq LEADING:10 TRAILING:10 SLIDINGWINDOW:4:30 MINLEN:50 ;

And loop through your files for $Reads 1 and $Reads2 where $Reads1 is for R1 etc...

ADD COMMENTlink modified 6 months ago • written 6 months ago by SaltedPork100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1201 users visited in the last hour