RNA sketching

[drtamermansour]

The WGS and metagenomic samples with high 'relative mapping rate' turned to be RNAseq and meta-transcrptomic. We can use this a a standard QC function:

1. We need a sketch of the canine RNA fasta (to include the splicing k-mer). We can download from NCBI like the genome and GFF. Here is the link: https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_000002285.3/download?include_annotation_type=RNA_FASTA&include_annotation_type=SEQUENCE_REPORT&hydrated=FULLY_HYDRATED
2. Now we can intersect with unmapped k-mers. Only RNA samples should show high intersection
3. It would be better if we downloaded and sketched some canine RNAseq projects (we already excluded 54 samples in our intial SRA search)