sRNAPipe query for input fasta files

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Hello there,

I am trying to use the sRNApipe tool for small RNA seq analysis from Mouse samples. Can you please tell me where I can the required source fasta files for the different input requirements of this tool - namely the reference genome, transcripts, transposable elements, miRNAs, snRNAs, rRNA, tRNAs? It would be great if you could provide the link(s) from where I can download these files.

With regards,
Abishek

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Hi @srinivasa_abishek

Does this help? FAQ: Extended Help for Differential Expression Analysis Tools

Reference genome

UCSC is a good source for the reference genome fasta, and most public servers will already have that loaded and indexed with tools.

Reference Annotation
Reference Transcripts or Features

UCSC and Genecode are both good sources for the transcripts fasta and annotations GTF. This is the Genecode link → https://www.gencodegenes.org/. Genecode annotations are based on the same version of the mouse genomes as UCSC’s are.

  • GTF → At UCSC, the annotations in the Downloads area represent gene tracks defined in the main browser application. At Genecode, see the descriptions directly where the annotation files are located.
  • Transcript fasta → It is very important that the transcripts are related to the annotation you decide to use.
    • The tool gffread can be used to extract the fasta from the genomic based on specific annotated regions (based on the genomic). For data like curated RefSeq transcripts, get the UCSC annotation and transcripts in the Downloads area (based on curated data, might differ from genomic extraction).

Hope this helps! :slight_smile: