Hi, I have sequenced 3 males and 3 females fish gonad miRNA using Illumina Hiseq.
Is there any software that we can input the raw Fastq files in it and it performs barcode removing, and clean and remove other small RNAs and then perform differential expression analysis ? it is a de novo study and my species has not any reference genome.
I want to find sexually DE miRNAs?
I have the same RNA-seq data, too. And I have used Trinity program for assembling them. Thank you in advance