RNA-seq and ORF57 CLIP-seq data analysis
Total RNA from 4 replicates of BCBL-1 WT clone B4 and 57KO clone #6 cells were isolated by TriPure Reagent (Roche) 24 h after induction with VA. The genomic DNA was removed using RNeasy Mini Kit (Qiagen) on-column DNase-treatment. Total RNA-seq libraries were prepared with TruSeq Stranded Total RNA Library Kit and subjected to pair-end sequencing

PLOS PATHOGENS
KSHV RNA splicing and ORF57 using HiSeq3000/4000 chemistry and 2 × 150 nts modality. Reads were trimmed with CutAdapt v.1.18 and mapped to human GRCh38 (hg38)/KSHV (GenBank Acc. No. HQ404500) chimeric genome using STAR aligner v.2.7.0f. [23]. The changes of viral gene expression between individual groups were determined by the Limma Voom package using reads mapped to annotated KSHV ORFs. The splice reads mapped to the KSHV genome were extracted to identify unique viral splice junctions. The distribution of splicing junction along the KSHV genome was visualized using Integrative Genomics Viewer (IGV, Broad Institute). The strength of viral splicing sites was calculated using the MaxEntScan::score algorithm [32]. The original sequence libraries were deposited in NCBI's GEO repository (Acc. No. GSE194239). ORF57 CLIP-seq was detailed in our previous publication [53] and the obtained sequence libraries are publicly available in NCBI's GEO depository (Acc. No. GSE179726). The obtained reads were mapped to chimeric human GRCh37 (hg19)/KSHV (GenBank Acc. No. U75698) reference genome using STAR aligner (version 2.7.6a) [23] and visualizes by IGV.

### Language ###
English

### Assessment ###
We can ask about the specific software used for genome visualization, which is a clear and singular piece of information from the text.

### Query ###
What software tool can I use to visualize genomic data distribution?
What software tool can I use to visualize genomic data distribution?