I am new to RNA-Seq data analysis. Sorry for very basic question :)
I was given a task to generate read counts for a published dataset. I have followed the below pipeline and generated read counts. But in this pipeline there is no preprocessing of fastq files like removal of ribosome sequences. are these fastq files have ribosomal sequences? Any other pre-processing always required?
bowtie2-build TAIR10_chr_all.fas Araindex bowtie2 -x Araindex -1 SRR6371142_1.fastq -2 SRR6371142_2.fastq -S SRR6371142.SAM sam.files <- list.files(path = "sf_SHARED-VB/", pattern = ".SAM$", full.names = TRUE) fc <- featureCounts(sam.files, annot.ext="Arabidopsis_thaliana.TAIR10.41.gtf",isPairedEnd=TRUE,isGTFAnnotationFile=TRUE)
Thanks for help!