Hi Friends,
I am having this problem with Illumina Hiseq (v. 1.9) paired end libraries (150nt reads). The number of surviving reads after trimming are very low.
This is my command:
My adapter FASTA file:
Stats from trimmomatic:
I would appreciate your help and/or suggestions.
BADE
I am having this problem with Illumina Hiseq (v. 1.9) paired end libraries (150nt reads). The number of surviving reads after trimming are very low.
This is my command:
Code:
java -jar trimmomatic-0.32.jar PE -threads 28 -phred33 WT_CTTGTA_L001_R1_001.fastq WT_CTTGTA_L001_R2_001.fastq Out_paired_WT_CTTGTA_L001_R1_001.fastq.gz Out_unpaired_WT_CTTGTA_L001_R1_001.fastq.gz Out_paired_WT_CTTGTA_L001_R2_001.fastq.gz Out_unpaired_WT_CTTGTA_L001_R2_001.fastq.gz ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
>PrefixPE/1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PrefixPE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>ReadThrough_PE/1
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
>ReadThrough_PE/2
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
>PCR_Primer/1.1/1
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTA
>PCR_Primer/1.2/1
ATCTCGTATGCCGTCTTCTGCTTG
>PCR_Primer/1.1/2
CAAGCAGAAGACGGCATACGAGAT
>PCR_Primer/1.2/2
TAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
TACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PrefixPE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>ReadThrough_PE/1
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
>ReadThrough_PE/2
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
>PCR_Primer/1.1/1
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTA
>PCR_Primer/1.2/1
ATCTCGTATGCCGTCTTCTGCTTG
>PCR_Primer/1.1/2
CAAGCAGAAGACGGCATACGAGAT
>PCR_Primer/1.2/2
TAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'ATCTCGTATGCCGTCTTCTGCTTG'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTA'
Using Long Clipping Sequence: 'TAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGAT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 3 forward only sequences, 3 reverse only sequences
Input Read Pairs: 22060013 Both Surviving: 14586934 (66.12%) Forward Only Surviving: 6580960 (29.83%) Reverse Only Surviving: 237640 (1.08%) Dropped: 654479 (2.97%)
TrimmomaticPE: Completed successfully
Using Long Clipping Sequence: 'ATCTCGTATGCCGTCTTCTGCTTG'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTA'
Using Long Clipping Sequence: 'TAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGAT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 3 forward only sequences, 3 reverse only sequences
Input Read Pairs: 22060013 Both Surviving: 14586934 (66.12%) Forward Only Surviving: 6580960 (29.83%) Reverse Only Surviving: 237640 (1.08%) Dropped: 654479 (2.97%)
TrimmomaticPE: Completed successfully
BADE
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