Question: Visualizing Transcriptional Structural variants in bedpe format
gravatar for mah19
2.8 years ago by
mah190 wrote:

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

tsv • 1.2k views
ADD COMMENTlink modified 2.8 years ago by Hussain Ather940 • written 2.8 years ago by mah190
gravatar for Hussain Ather
2.8 years ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

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

ADD COMMENTlink written 2.8 years ago by Hussain Ather940

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

ADD REPLYlink written 2.8 years ago by mah190
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