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Low-level RNA-seq class #41

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jayhesselberth opened this issue Jan 29, 2025 · 0 comments
Open

Low-level RNA-seq class #41

jayhesselberth opened this issue Jan 29, 2025 · 0 comments

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@jayhesselberth
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jayhesselberth commented Jan 29, 2025 •
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Based on student feedback (from 2023/24) we could carve out 1 class (likely at the end of the RNA block) that focuses on lower-level analysis of RNA sequencing data (as an example), focusing on command-line tools.

  1. Data download (get FASTQ from GEO, curl)
  2. Reference download (get Gencode FASTA, curl)
  3. Reference building (STAR index, STAR)
  4. Alignment (STAR alignment STAR)
  5. (optional) Pseudo-alignment (salmon)
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