use Trimmomatic to remove adapter

Question

[yueli7]

Hello,

I have a dataset of RNA sequencing.

I used the command to remove the adapter. After fastqc, it still has failure in Adapter Content.

Thanks in advance for great help!

Best,

Yue

yliTrimmomatic-0.39$ java -jar trimmomatic-0.39.jar PE P10_1.txt.gz P10_2.txt.gz P10_1_paired.fastq.gz P10_1_unpaired.fastq.gz P10_2_paired.fastq.gz P10_2_unpaired.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

[lieven.sterck]

Would it be possible to post the runtime output of trimmomatic here?

The image you show is one of a fastqc run after adapter removing, correct? (and you did not mix up files for example?)

[yueli7]

Hello Lieven.sterck,

Thank you so much for your response!

I should upload the file of NexteraPE-PE.fa.

Thank you again!

Best,

Yue

>PrefixNX/1
AGATGTGTATAAGAGACAG
>PrefixNX/2
AGATGTGTATAAGAGACAG
>Trans1
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
>Trans1_rc
CTGTCTCTTATACACATCTGACGCTGCCGACGA
>Trans2
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
>Trans2_rc
CTGTCTCTTATACACATCTCCGAGCCCACGAGAC