Identification of piRNA/siRNAs from small RNA-seq data
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15 months ago
jkkbuddika ▴ 180

Hi,

I am in the process of analyzing a collection of small RNA datasets from flies (Drosophila melanogaster). So far this is what I have done:

  1. Trim adaptors using cutadapt and extract 18-30nt long sequences.
  2. Align to the Drosophila genome using Bowtie (not Bowtie2): Reads with at least one alignment 80-85%
  3. Count miRNAs using featureCounts using miRBase annotations.
  4. I also use ShortStack to identify potential novel small RNAs.

Now I want to identify piRNAs and siRNAs from my data. I see there are a couple of piRNA databases with piRNA data (like piRNAdb and piRBase). Can I use a GTF from one of these databases to identify piRNAs? How about siRNAs?

Thanks,

KB

rna-seq gene alignment next-gen sequencing • 523 views
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An important point here is to make sure you do not loose reads with multi mapping as many piRNAs are similar sequences.

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