icSHAPE RNA Struct Track Settings
icSHAPE RNA Structure   (All mRNA and EST tracks)

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 icSHAPE In-vitro  icSHAPE In-vitro   Schema 
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This track shows normalized icSHAPE reactivity data of in vivo and in vitro SARS-CoV-2 experiments.


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.

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.


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