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Fig. 1 | BMC Bioinformatics

Fig. 1

From: PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data

Fig. 1

PΨFinder workflow. A Overall workflow of PΨFinder. If the input data are fastq files, these will be aligned using STAR. The resulting BAM file (input as default) is annotated with known PΨgs. Spliced reads, chimeric pairs and chimeric reads are extracted and combined to detect novel PΨgs and predict its insertion site. Results are displayed as text and html files. Different plots may be generated, including circular and linear layouts, scatter plots and summary dotplots. B Detection of a PΨg. Blue rectangles depict coding regions. Reads are depicted as arrows. Gray arrows refer to spliced reads, with dotted lines showing the splicing event. C Detection of the PΨg-insertion site. Blue arrows show reads mapping to the PΨg or portion of the PΨg, while red arrows show reads mapping to the PΨg insertion site or portion of the PΨg insertion site. Solid gray lines deem two reads as a pair. PΨFinder reports positions marked with dashed arrows. CR chimeric read, CP chimeric pair

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