The pipeline will go from process sequences to and using htseq counts will quantify expression on genes UTR and CDS, and in addition it will find the peaks and shift them.
Need to have a genome from igenomes bowtie2index , genome gtf file, rRNA indexed for bowtie (descibed described below how to have such a file) and gtf file of UTR and CDS explained below how to prepare.
and chromosome size file such as hg38.chrom.sizes
rRNA indexed for bowtie
human U:\10and12drugs\rRNA
mouse U:\RPanalysis\rRNA
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