Visualizing Transcriptional Structural variants in bedpe format

Question

[MoHallal]

Hello, I have generated transcription structural variant files from RNA-Seq data in Bedpe format by running chimeric Bam files with SQUID. Is there a way to visualize these files and locate the variants on their relevant positions on the reference genome, ie some tool that can show the variants and how they connect distinct chromosomal regions together ? Thank you

Answer 1

[Hussain Ather]

You could try visualizing them in IGV or the UCSC Genome browser.

[MoHallal]

Hello Hussain, Thank you for your reply. Unless I m doing something wrong IGV will only show you one section of the variant at as it aligns to its location on the genome. I am interested to see how TSVs connect different genomic regions together in a graphical manner. Thanks