I am new to the Bioinformatics. I want to find differentially expressed genes from a non model species. I used trinity for the de novo assembly and used RSEM to count the reads. I used fastq files as input for RSEM not bam files (sorted by name). In the DESeq2 manual it says, name sorted bam files are necessary to run the analysis for paired end reads, So can I use the RSEM output that I have, for DESeq2 or not?
Thank you so much for your time and help.