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  • cleaning cp, mt and rRNA from reads

    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.

  • #2
    align the reads against a database of cp, mt and rRNA and keep the unaligned ones for further analysis

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    • #3
      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 regions

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      • #4
        Also, using the bowtie parameter -un; it will save the unmapped reads from your non-desirable refs.

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