2 hours ago by
Hello every one I have paired end illumina reads for chip-seq analysis. Fastqc report adapter content and all so per sequence GC content not passing, I tried trimmomatic but still i am getting same result. can anyone suggest me how can I resolve this problem
command I tried
trimmomatic PE read1.fastq.gz read2.fastq.gz filt_read1.fastq.gz read2.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 HEADCROP:20
after this still did not pass the adapter content and per sequence GC content
TruSeq3-PE.fa file contains collected from different biostar threads
Illumina_Universal_Adapter (copied from FastQC data files)
AGATCGGAAGAG
TruSeq_Universal_Adapter
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
TruSeq_Universal_Adapter_RC
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
TruSeq_Index_Adapter
GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
TruSeq_Index_Adapter_RC
CAAGCAGAAGACGGCATACGAGAT
Can any one suggest me how can I resolve this Thank you
result image
drive.google.com/file/d/15SC0r31eJFDYs9Rowysxd4853iO1XQBW/view?usp=sharing, drive.google.com/file/d/1msoloMqHHBfCTuAyAqPXxJYyomZBeVdX/view?usp=sharing
Thank you
