Raw read processing using trimmomatic

Question

[CHINMAYA]

i work on paper where author use Illumina HiSeq 4000 platform using 100 bp paired-end strategy for transcription sequencing.

for raw read processing they use criteria with tool :- (>20% of the bases with a phred quality score < 10) using Trimmomatic v0.35

i was donig same with this code but the result is not same that on the paper.`

fastq-dump --split-3  srr.sra --gzip

java -jar trimmomatic-0.35.jar PE -threads 8 -summary statsSummaryFile 1.fastq.gz 2.fastq.gz 1_paired.fq.gz 1_unpaired.fq.gz 2_paired.fq.gz 2_unpaired.fq.gz ILLUMINACLIP:TruSeq2-PE.fa:2:30:7:1:keepBothReads SLIDINGWINDOW:4:20

any help?

[boczniak767]

Do you have exact command used by the author? I guess that not all details was presented in the paper. You can always ask the corresponding author.