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  • Small RNA Read Counts

    New to NGS data, currently analyzing small RNA seq data with emphasis on piRNAs, looking to eventually do differential expression analysis. I have my reads aligned, but now a little unsure of how best to go about getting total read counts for the areas of the genome I am interested in. I have ~500 genomic coordinates for regions of interest which should be areas of piRNA production.

    I'm thinking of using bedtools to get a count of alignments which overlap with my ~500 regions. Is there a better way to do this? Suggestions and useful commands/parameters/programs very welcome.

    Cheers
    Last edited by WHP; 04-28-2014, 11:53 AM.

  • #2
    htseq-count is often used for this.

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    • #3
      Originally posted by WHP View Post
      New to NGS data, currently analyzing small RNA seq data with emphasis on piRNAs, looking to eventually do differential expression analysis. I have my reads aligned, but now a little unsure of how best to go about getting total read counts for the areas of the genome I am interested in. I have ~500 genomic coordinates for regions of interest which should be areas of piRNA production.

      I'm thinking of using bedtools to get a count of alignments which overlap with my ~500 regions. Is there a better way to do this? Suggestions and useful commands/parameters/programs very welcome.

      Cheers
      Hi, did you resolve your problem? I come across the same question.

      Comment

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