Trimmomatic on Zipped Files

[arcolombo698]

Hello.

I have Sample_R1.fastq.gz files. I submitted a run to trim the data using

If you notice below that I included the extension .gz for each fastq. I just want to make sure that Trimmomatic can run on .gz files.


java -classpath /auto/rcf-proj/sa1/software/Trimmomatic-0.22/trimmomatic-0.22.jar org.usadellab.trimmomatic.TrimmomaticPE -threads 16 -phred33 Sample-122_S3_R1.fastq.gz sample-122_S3_R2.fastq.gz paired_trimmed_sample-122_S3_R1.fastq.gz unpaired_trimmed_sample-122_S3_R1.fastq.gz paired_trimmed_sample-122_S3_R2.fastq.gz unpaired_trimmed_sample-122_S3_R2.fastq.gz SLIDINGWINDOW:4:20 MINLEN:30

[usad]

Hi

yes it does (and bz2 as well), no need to unzip the fastq files.

Best Wishes
Björn

[arcolombo698]

Alignment on zipped fastq

Hello.

I posted a new thread asking this question, but I just wish to ask you Bjorn.

Does alignment work on zipped data??

[dpryan]

Usually yes (at least gzipped).

Realistically, everything can be made to support compressed input using FIFOs, if it's not built in (though it typically is).