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Trimmomatic drops 50% of reads #51

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RacheliHadjez opened this issue Jun 25, 2023 · 0 comments
Open

Trimmomatic drops 50% of reads #51

RacheliHadjez opened this issue Jun 25, 2023 · 0 comments

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@RacheliHadjez
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Hello,
I am trying to trim adapters of my PacBio data with trimmomatic.
This is my command:

module load miniconda/miniconda3-4.7.12
module load idba

java -jar /dorotheeh/trimmomatic/trimmomatic-0.39.jar SE -phred33 PBrnaQ20.ccs.fastq.gz PBrnatrimmed.fq.gz ILLUMINACLIP:pacbio_vectors_db.fasta:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:400

And it trimmed more than half of my reads:
Using Long Clipping Sequence: 'TTCGTCACCATAGTTGCGTCTCATG'
ILLUMINACLIP: Using 0 prefix pairs, 3 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Reads: 4826329 Surviving: 2282550 (47.29%) Dropped: 2543779 (52.71%)
TrimmomaticSE: Completed successfully

Could someone explain what should I fix in the command?

Thank you!

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