Schema for Kim RNA Modific. - Kim et al. Nanopore RNA Modifications: 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
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart25355Start position in chromosome
chromEnd25358End position in chromosome
name25357Position of modified nucleotide
score999Score from 0-1000, typically derived from total of median value from all categories
strand++ or - for strand. Use . if not applicable
name2GCUCAAASequence context of modified nucleotide
expCount10Number of categories
expScores0.312,0.146,0.571,0.0,0.0,0.0,0.0,0.0,0.0,0.0Comma separated list of category values
_dataOffset291Offset of sample data in data matrix file, for boxplot on details page
_dataLen51Length of sample data row in data matrix file

Sample Rows
 
chromchromStartchromEndnamescorestrandname2expCountexpScores_dataOffset_dataLen
NC_045512v2253552535825357999+GCUCAAA100.312,0.146,0.571,0.0,0.0,0.0,0.0,0.0,0.0,0.029151
NC_045512v2254582546125460999+AUGCUAC100.317,0.356,0.332,0.0,0.0,0.0,0.333,0.0,0.0,0.034353
NC_045512v2260562605926058999+AGACACU100.317,0.291,0.31,0.0,0.4,0.0,0.0,0.0,0.0,0.039750
NC_045512v2262952629826297999+UACUUCU100.169,0.153,0.151,0.321,0.0888,0.0,0.0,0.0,0.0,0.044856
NC_045512v2267292673226731999+CUGUUUA100.372,0.311,0.327,0.372,0.363,0.333,0.4,0.0,0.0,0.2550558
NC_045512v2271042710727106999+CUGCAUA100.304,0.281,0.289,0.311,0.305,0.32,0.333,0.0,0.0,0.056458
NC_045512v2271632716627165999+AGUGACA100.252,0.302,0.258,0.228,0.236,0.224,0.286,0.0,0.0,0.062359
NC_045512v2272662726927268999+UUUAAAG100.178,0.0779,0.0914,0.187,0.221,0.358,0.25,0.0,0.0,0.068360
NC_045512v2273032730627305999+ACCUCAU100.106,0.311,0.164,0.12,0.142,0.128,0.222,0.0,0.0,0.074458
NC_045512v2274842748727486999+UUUAAAA100.202,0.108,0.114,0.177,0.186,0.258,0.243,0.353,0.0,0.22280363

Kim RNA Modific. (kimRnaMod) Track Description
 

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.

Data Access

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.

Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:

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.

Credits

Thanks to Hyeshik Chang for preparing and sharing custom tracks.

References

The architecture of SARS-CoV-2 transcriptome. Cell 2020. pre-proof