Description
This track shows normalized icSHAPE reactivity data of in vivo and in vitro SARS-CoV-2 experiments.
Methods
icSHAPE scores were provided by Qiangfeng Cliff Zhang and converted to bigWig.
The first five nucleotides of the genome and the last thirty nucleotides have
no data due to technical defects (on the 5' and 3' ends of the virus) or insufficient
sequencing depth. The icSHAPE score is distributed between 0 and 1.
Data Access
You can download the bigWig file underlying this track (icshape/*.bw) from our
Download Server. The data can be explored interactively with the
Table Browser
or the Data Integrator. The data can be
accessed from scripts through our API.
http://api.genome.ucsc.edu/getData/track?genome=wuhCor1;track=icshapeInvitro;chrom=NC_045512v2;start=100;end=7875
Command-line extraction can be accomplished using an example like the following command:
bigWigToWig -udcDir=. -chrom=NC_045512v2 -start=100 end=7875 https://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/bbi/icshape/invivo.bigWig myOutput.wig
Please refer to our mailing list archives for questions, or our
Data Access FAQ for more
information.
References
Lei Sun, Pan Li, Xiaohui Ju, Jian Rao, Wenze Huang, Shaojun Zhang, Tuanlin Xiong, Kui Xu, Xiaolin Zhou, Lili Ren, Qiang Ding, Jianwei Wang, Qiangfeng Cliff Zhang
"In vivo structural characterization of the whole SARS-CoV-2 RNA genome identifies host cell target proteins vulnerable to re-purposed drugs", Biorxiv July 8 2020
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