I'm new to RNA-seq data analysis..
I downloaded 6 samples (3 for every condition) and I ran QC on them and had to trim the adaptors and poor reads.. what happened is that 3 replicates of one condition received (aggressive trimming) and removed around 15% of reads as an average. while 7% of reads have been thrown from the other condition replicates.
now removal of 15% will affect my downstream analysis, so is there any recommendations to improve the trimming procedure or this normal because of issues in the original row data ??
my trimmomatic command:
java -jar ~/Desktop/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 SRR11771_1.fastq SRR11771_2.fastq TRMD_SRR11771_1_paired.fastq TRMD_SRR11771_1_unpaired.fastq TRMD_SRR11771_2_paired.fastq TRMD_SRR11771_2_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
my plan is to do exon-centric analysis using tophat and star as aligners and miso, mats and suppa for differential splicing analyses..
Your help is really appreciated.