/volume2/web/Atumefaciens/20220217-cvir-lncRNA_subsetting

Generation of lncRNA files from C.virginica NCBI GCF_002022765.2_C_virginica-3.0 genome files. 

- checksums.md5: List of MD5 checksums for files in this directory.

- GCF_002022765.2_C_virginica-3.0_lncRNA.bed: BED file of lncRNAs.

- GCF_002022765.2_C_virginica-3.0_lncRNA.fa: FastA seqs of lncRNAs. Consists of spliced exons. Exon coordinates are listed in each sequence definition line.

- GCF_002022765.2_C_virginica-3.0_lncRNA.fa.fai: FastA index file - created with samtools faidx.

- GCF_002022765.2_C_virginica-3.0_lncRNA.gff: GFF file of lncRNAs. Extracted from NCBI CF_002022765.2_C_virginica-3.0_genomic.gff using gtf_extract from gffutils.

- GCF_002022765.2_C_virginica-3.0_lncRNA.gtf: GTF file of lncRNAs. Extracted from GCF_002022765.2_C_virginica-3.0_lncRNA.gff from using gffread.

- gffread_lncRNA-fasta-extraction.stderr: Standard error output from gffread FastA extraction.

- gffread-lncRNA_gff-to-lncRNA_gtf.stderr: Standard error output from gffread gtf extraction.


Notebook:

https://robertslab.github.io/sams-notebook/2022/02/17/Data-Wrangling-C.virginica-lncRNA-Extractions-from-NCBI-GCF_002022765.2-Using-GffRead.html

Jupyter Notebook: 

https://nbviewer.ipython.org/github/RobertsLab/code/blob/master/notebooks/sam/20220217-cvir-lncRNA_subsetting.ipynb