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  • How to remove transcripts overlapping with annotated genes

    Hello,
    Im trying to see the novel lnc RNA for not well annotated genome as very few lnRNA is known in this genome.
    So what I'm doing is to align the fastq file with the whole genome fastafile to get the SAM file.
    then annotate the SAM file with the stringtie and get the GTF file.
    Now I want to remove this annotated transcript
    What do you think?
    and How to do it?

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