Can anyone help me to figure out how to clean my raw reads from cp, mt and rRNA reads? I have Hi-seq data for RNA samples.
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align the reads against a database of cp, mt and rRNA and keep the unaligned ones for further analysis -
If you are using tophat/cufflinks you can remove them during the analysis. If you are mapping with something else then EdgeR or DESeq then just format the genome annotation file to exclude those regionsComment
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Also, using the bowtie parameter -un; it will save the unmapped reads from your non-desirable refs.Comment
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