Schema for Subgenomic RNA Modif. - Subgenomic RNA Modifications from Kim et al. 2020: gRNA S 3a E M 6 7a 7b 8 N
Database: wuhCor1 Primary Table: kimRnaMod Data last updated: 2020-04-10|
Big Bed File: /gbdb/wuhCor1/bbi/kim2020/kim-scv2-drs-modifications.bb
Item Count: 41
Format description: BED6+5 with additional fields for category count and median values, and sample matrix fields
|chrom||NC_045512v2||Reference sequence chromosome or scaffold|
|chromStart||25355||Start position in chromosome|
|chromEnd||25358||End position in chromosome|
|name||25357||Position of modified nucleotide|
|score||999||Score from 0-1000, typically derived from total of median value from all categories|
|strand||+||+ or - for strand. Use . if not applicable|
|name2||GCUCAAA||Sequence context of modified nucleotide|
|expCount||10||Number of categories|
|expScores||0.312,0.146,0.571,0.0,0.0,0.0,0.0,0.0,0.0,0.0||Comma separated list of category values|
|_dataOffset||291||Offset of sample data in data matrix file, for boxplot on details page|
|_dataLen||51||Length of sample data row in data matrix file|
Subgenomic RNA Modif. (kimRnaMod) Track Description
This track shows the locations of RNA-modifications as determined by Nanopore sequencing
Kim et al, Cell 2020.
Display Conventions and Configuration
Very small tickmarks indicate the position of the RNA modifications on the
genome. One has to zoom in to basepair level detail to see their exact extent. A
small barchart over the tick indicates the fraction of transcripts that are modified
relative to the un-modified transcripts. E.g. frac=0.3 means that 30% of the transcripts
were modified. There is one barchart per transcript.
The raw data can be explored interactively with the
Table Browser, or combined with other datasets in the
Data Integrator tool.
For automated analysis, the genome annotation is stored in
a bigBed file that can be downloaded from
the download server.
be converted from binary to ASCII text by our command-line tool bigBedToBed.
Instructions for downloading this command can be found on our
The tool can also be used to obtain features within a given range without downloading the file,
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/bbi/kim2020.bb -chrom=NC_045512v2 -start=0 -end=29902 stdout
Please refer to our
mailing list archives
for questions, or our
Data Access FAQ
for more information.
Thanks to Hyeshik Chang for preparing and sharing custom tracks.
The architecture of SARS-CoV-2 transcriptome.
Cell 2020. pre-proof