Data Wrangling - C.virginica lncRNA Extractions from NCBI GCF_002022765.2 Using GffRead

Continuing to work on our Crassostrea virginica (Eastern oyster) project examining the effects of OA on female and male gonads (GitHub repo), Steven tasked me with parsing out long, non-coding RNAs (GitHub Issue). To do so, I relied on the NCBI genome and associated files/annotations. I used GffRead, GFFutils, and samtools. The process was documented in the followng Jupyter Notebook:

• 20220217-cvir-lncRNA_subsetting.ipynb (GitHub)

• 20220217-cvir-lncRNA_subsetting.ipynb (NBviewer)

---

RESULTS

Output folder:

• 20220217-cvir-lncRNA_subsetting/

  • GCF_002022765.2_C_virginica-3.0_lncRNA.bed (640K)

    • MD5: 28de37c9ee1308ac1175397d16b3aafe

  • GCF_002022765.2_C_virginica-3.0_lncRNA.fa (25M)

    • MD5: 7fac9e7191915f763cc7f5d22838ac25

  • GCF_002022765.2_C_virginica-3.0_lncRNA.fa.fai (180K)

    • MD5: 1b43db284950abc07afb5f50164fb264

  • GCF_002022765.2_C_virginica-3.0_lncRNA.gff (2.1M)

    • MD5: 00755b8c80166cdec94b09f231ef440a

  • GCF_002022765.2_C_virginica-3.0_lncRNA.gtf (1.3M)

    • MD5: dedab056acd679cf4eab83629882ee10