From: RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Attribute Name | Description |
---|---|
seqnames | Chromosome on which the aligned read is mapped. |
ranges | Start and end position of the alignment in genomic coordinates. |
strand | Strand to which the aligned read is mapped. |
sample | Sample name from which the alignment originates. |
exp | Experiment type of the sample from which the alignment originates, either ‘Ribo’ for Ribo-seq, or ‘RNA’ for RNA-seq. |
length | Length of the aligned read in nucleotides. |
gene | Gene to which the read is mapped. Corresponds to Gene IDs within the provided annotation file. ‘Other’ if not mapped within a gene. |
feature | Feature type to which the read is mapped. Feature types correspond to those included in the user-provided annotation file. |
pos | Genomic position of alignment based on p-site adjustment. |
start_dist | Distance from transcription start site (TSS) of a gene to p-site position, in transcript coordinates (with introns removed). The major isoform of each gene is used to calculate this distance. |
end_dist | Distance from p-site position to translation stop codon (TSC) of a gene, in transcript coordinates (with introns removed). The major isoform of each gene is used to calculate this distance. |
gc | The percentage of nucleotides in the aligned read which are G’s or C’s. |
mapq | The mapq score of the alignment. Typically, alignments with a mapq score of 50 are considered uniquely mapped, while all other scores are considered multi-mapping. |
frame | The trinucleotide frame of a read’s p-site, relative to the TSS of the gene’s major isoform. Reads that map within an mRNA are assigned either a 0, 1, or 2, while reads which map outside the mRNA are assigned ‘none’. |