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)

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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