Question: How to trim both pair end reads and remove low quality reads
1
gravatar for Bioinfonext
13 months ago by
Bioinfonext200
Korea
Bioinfonext200 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 • 562 views
ADD COMMENTlink modified 11 months ago by SaltedPork100 • written 13 months ago by Bioinfonext200
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 13 months ago by ATpoint29k

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

ADD REPLYlink written 13 months ago by Kevin Blighe55k

And how poor is "very poor"?

ADD REPLYlink written 13 months ago by finswimmer13k
0
gravatar for SaltedPork
11 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 11 months ago • written 11 months ago by SaltedPork100
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