Table 2 CGDV supported data types, corresponding file formats and description of the plot
From: CGDV: a webtool for circular visualization of genomics and transcriptomics data
S.No. | Data type | File format | Circular plot |
|---|---|---|---|
1 | VCF | vcf version 4.1 | SNP and InDel with their sequencing depth |
2 | CNVnator output | raw output of CNVnator | Amplification and deletion with their size |
3 | ChIPSeq | raw output from MACS in XLS format | Peaks and tag density with their p-value |
4 | Gene fusion output | raw output from fusion inspector | Links between various genes which are fused together with color intensity based upon number of reads supporting each fusion event |
5 | Cuffdiff output | raw output from Cuffdiff | FPKM values per gene /isoform |
6 | BED | Extended BED upto 12 data columns | Expression values per genome coordinate |
7 | Matrix-links | Data in a matrix format | Links between data in the row and column |
8 | BLAST output | BLAST output data in a tabular format (BLAST run with –m8 option) | Links between similarity among homologous sequences |