Trimmomatic destroys right-hand paired-end sequences, how to avoid?

Question

[dec986]

Hello everyone,

I am attempting to run trimmomatic, but am having issues:

1) how to identify necessary adapters? TrimGalore does this automatically, the only way I can think of to do this is to automatically load everything in the database, or just read TrimGalore's output, is this practical?

2) I have been running trimmomatic thus (with perl scalar variables) using the command recommended on their website:

java -jar $trimmomatic PE -phred33 $fq1 $fq2 $qc1 $qc2 $unpaired1 $unpaired2 ILLUMINACLIP:$clip:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 > $dir/$directory.trimmomatic.stdout 2> $dir/$directory.trimmomatic.stderr

but this eliminates about 96% of the right-hand reads while retaining about 96% in the left-hand read, inexplicably. How can I clip without destroying the right-hand reads?

Answer 1

[Martombo]

I guess you're looking at the wrong file since the output files should be specified in the following order (using your variables):

$qc1 $unpaired1 $qc2 $unpaired2