GSE232514 Processing Pipeline

RNA-Seq code_examples 5 steps

Publication

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.

Nature communications (2024) — PMID 39152130

Dataset

GSE232514

Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (2)

Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.

Processing Steps

Generate Jupyter Notebook
  1. 1

    remove adapter with Cutadapt

    cutadapt
  2. 2

    align to human genome using STAR 2.7.6a

    STAR v2.7.6a
  3. 3

    align unmapped reads from above to 12X MS2 stem-loop reporter mRNA using STAR 2.7.6a

    STAR v2.7.6a
  4. 4

    SAILOR analysis of data for C-to-U edits

    SAILOR
  5. 5

    SAILOR analysis of data for A-to-I edits

    SAILOR

Tools Used

STAR SAILOR
Raw Source Text 
remove adapter with Cutadapt
align to human genome using STAR 2.7.6a
align unmapped reads from above to 12X MS2 stem-loop reporter mRNA using STAR 2.7.6a
SAILOR analysis of data for C-to-U edits
SAILOR analysis of data for A-to-I edits
Assembly: GRCh38
Assembly: 12X MS2 stem-loop reporter mRNA
Supplementary files format and content: The processed data files are in .bed format. They contain SAILOR-identified C-to-U or A-to-I edit information for endogenous transcripts (*non.construct.bed) and the 12X stem-loop-bearing-bearing reporter mRNA (*reporter.construct.bed).
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