[mslider]

yes i have made adapters file myself because i have not find the best file corresponding to ScripSeq-v2 protocol in trimmomatic manual, in ScripSeq-v2 protocol it was mentionned this adapter:

5' CAAGCAGAAGACGGCATACGAGAT index (NNNNNN) GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT3'

and in my read 1 you find the reverse as:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG

i don't know if TruSeq3-PE-2.fa adapter file was the good option to clean my PE reads.

[a.vhd]

Hi all, I have tried Trimmomatic using the following command line:

java -jar trimmomatic-0.33.jar PE OrAe0G_read1.fastq OrAe0G_read2.fastq OrAe0G_read1_pe.fastq OrAe0G_read1_se.fastq OrAe0G_read2_pe.fastq OrAe0G_read2_se.fastq HEADCROP:13 TRAILING:5 ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 MINLEN:20

and running in to the following error:

Caused by: java.lang.ArrayIndexOutOfBoundsException: 58
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer$IlluminaPrefix

Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 58
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.usadellab.trimmomatic.threading.TrimStatsWorker.run(TrimStatsWork

Thanks alot,