Analysis of RNA II: RiboSeq, and other things
SARS-COV-2 COVID-19 RNAseq
Potentially interesting sites
This only works for PSU-based people
Open this spreadsheet.
It has the following columns:
- Group: People, to whom variants are assigned
- Sample: SRA accession
- CHROM: Reference genome (same for all rows)
- POS: Position of the variant in the genome (1-based)
- REF: Reference allele
- ALT: Alternative allele
- DP: Read depth
- AF: Alternative allele frequency
- SB: Strand bias as calculated by lofreq (0 = no strand bias)
- DP4: Strand-specific depth for reference and alternate allele observations (Forward reference, reverse reference, forward alternate, reverse alternate)
- IMPACT: functional impact of the substitution
- FUNCLASS: type of change
- EFFECT: effect of the change
- GENE: gene name
- CODON: codon
- type: type of variant (
S= SNP,I= Indel,M= MNP ) - GENE: gene name
- SITE: codon within the gene
- FEL: Is site identified by FEL as being under selection
- MEME: Is site identified by MEME as being under selection
- MEME.FRACTION: fraction of branches under selection
- CLASSIFICATION: Type of selection (also see here)
- SYN.SUBS: # synonymous substitutions
- NONSYN.SUBS: # non-synonymous substitutions
- COMPOSITION: composition of the alignment column
- PROPRETIES: amino acid change effect
- gSITE: Genomic coordinate
Instructions
- Find you group
- Perform additional filtering to create a conservative set of sites
- Find latest papers on the gene of interest
- See if any of the sites may be significant based on published biochemical or structural data.