Question: Trimmomatic adapter clipping removes many reads even if "keepBothReads" parameter is selected
0
gravatar for al-ash
2.1 years ago by
al-ash140
Japan/Okinawa/OIST
al-ash140 wrote:

I'm using Trimmomatic/0.33 to proces my raw Illumina reads. I've seen some adapter contamination with FASTQC so I first run Trimmomatic as follows:

java -jar trimmomatic-0.33.jar PE R1.fastq.gz R2.fastq.gz PR1.fastq.gz UPR1.fastq.gz PR2.fastq.gz UPR2.fastq.gz ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:1:keepBothReads

TruSeq3-PE-2.fa contains:

>PrefixPE/1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PrefixPE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>PE1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PE1_rc
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
>PE2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>PE2_rc
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

Trimmomatic reports back:

Input Read Pairs: 39618168 
Both Surviving: 28128581 (71.00%) 
Forward Only Surviving: 8927582 (22.53%) 
Reverse Only Surviving: 47164 (0.12%) 
Dropped: 2514841 (6.35%)

I was surprised that despite selecting the option to keep both reads even if they are palindromic via "keepBothReads" there is only 71% of "Both Surviving" : what might be the reads which did not survive? I can think of them only as entirely consisting of adapter sequences - is that correct? Thanks for any suggestion!

ADD COMMENTlink modified 2.0 years ago by finswimmer13k • written 2.1 years ago by al-ash140
1
gravatar for annsun89
2.0 years ago by
annsun8920
annsun8920 wrote:

Hi, I read the manual and <keepbothreads> is the name of the parameter but it's not how to set it. Instead, try

java -jar trimmomatic-0.33.jar PE R1.fastq.gz R2.fastq.gz PR1.fastq.gz UPR1.fastq.gz PR2.fastq.gz UPR2.fastq.gz ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:1:TRUE
ADD COMMENTlink written 2.0 years ago by annsun8920
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1934 users visited in the last hour