I am totally new in the bioinformatic analysis. I am working on a project that looks at DGE among different time treatments. Besides, there is no reference genome (meaning that I need a de novo assembly step).
So far, after struggling and navigating many website, I started using my terminal on MacBook and was able to do FastQC for the 118 reads (PE), I then followed this with MultiQC and both worked fine for me using the terminal. I am trying to go one step at a time. So I wanted to use trimmomatic to trim the reads but I failed!
I used the following command for one pair of reads and it worked but I do not know how to do this for the whole reads!
java -jar trimmomatic-0.39.jar PE -phred33 $i\1_R1_001.fastq.gz $i\1_R2_001.fastq.gz $i\1_R1_paired.fq.gz $i\1_R1_unpaired.fq.gz $i\1_R2_paired.fq.gz $i\1_R2_unpaired.fq.gz ILLUMINACLIP:contams_forward_rev.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
I tried adding * but it did not work.
java -jar trimmomatic-0.39.jar PE -phred33 -threads 4 /Users/mohamedhabib/Desktop/RNAseq/*_R1_001.fastq.gz *_R1_001.fastq.gz out_*_R1_001_P.fastq.gz out_*_R1_001_U.fastq.gz out_*_R2_001_P.fastq.gz *_R2_001_U.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:40:15
I will appreciate your help and advice on this specific topic and generally for further steps of analysis. Is there a template script (containing all the steps) that I can modify and use for my analysis?