RNA Sequencing Trimmomatic

Question

[neeshatripathi87]

Hello all, I have all my like 10-15 fastq file in 1 folder named combined and I need to trim that combined file. I tried some of the command like

TrimmomaticPE -phred33 /R1_001.fastq.gz /R2_001.fastq.gz /R1_pairedout /R1_unpairedout /R2_pairedout /R2_unpairedout ILLUMINACLIP:/TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 AVGQUAL:20

but that didn't work. Please give me some idea to trim.

[Matteo Schiavinato]

Is "TrimmomaticPE" a wrapper on your machine/HPC for Trimmomatic PE (note the space that separates the two)?

[WouterDeCoster]

Good catch, that too could be the issue.

[WouterDeCoster]

but that didn't work.

You need to be more precise. What happened? What didn't happen? Error message?

Anyway, if you used the command as you posted it here your paths are wrong because you are currently implying that your files are in the root folder.