Trimmomatic destroys right-hand paired-end sequences, how to avoid?
1
0
Entering edit mode
4.9 years ago
dec986 ▴ 340

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?

trimmomatic qc • 1.2k views
ADD COMMENT
3
Entering edit mode
4.9 years ago
Martombo ★ 3.0k

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
ADD COMMENT

Login before adding your answer.

Traffic: 2614 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6