Visualizations of chimeric connections in different chromosomes

Question

[lucas.caue.jacintho]

Hi everybody,

I just did a alignment by STAR, and I am pretty sure the BAM output has some chimeric connections among different chromosomes, but I do not know how to visualize them, whereas I do see the chimeric conections in the same chromosome. is this something related to the samples being paired-end instead single-end reads? Is there any way to see them on IGV? Because I could not find one that works.

Thanks in advance!.

Answer 1

[Pierre Lindenbaum]

I wrote a tool SV2SVG ( nevertheless, I have not used it often. ) : http://lindenb.github.io/jvarkit/SvToSVG.html

[lucas.caue.jacintho]

Thanks for your useful suggestion!I am trying to use your tool, but actually I am having some trouble to run the algorithm, I am not sure but maybe because i am dong RNAseq and not NGS. If you have any clue what is happening I'd appreciate it! T

Answer 2

[Vitis]

I'd suggest querying the alignments and find inter-chromosomal chimeric connections and visualize them with circos. It is possible to visualize intra-chromosomal connections within the same framework. And the unusual ones, if those are what you're after, would stand out in circos plots.

http://circos.ca

Answer 3

[Jim Robinson]

I concur with the circos suggestion, but if you use the default coloring scheme in IGV it will highlight alignments with color who's mate aligns to another chromosome. This assumes the BAM file is properly formatted with mate information. If you right click one of the colored alignments and select "View mate region" it will show you the genomic region of its mate in a new panel.