Question: Visualizing Transcriptional Structural variants in bedpe format
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gravatar for mah19
19 months ago by
mah190
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 • 786 views
ADD COMMENTlink modified 19 months ago by Hussain Ather920 • written 19 months ago by mah190
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gravatar for Hussain Ather
19 months ago by
Hussain Ather920
National Institutes of Health, Bethesda, MD
Hussain Ather920 wrote:

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

ADD COMMENTlink written 19 months ago by Hussain Ather920

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 19 months ago by mah190
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