Question: Visualizations of chimeric connections in different chromosomes
0
gravatar for lucas.caue.jacintho
6 weeks ago by
lucas.caue.jacintho30 wrote:

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!.

ADD COMMENTlink modified 4 weeks ago by Vitis2.3k • written 6 weeks ago by lucas.caue.jacintho30
1
gravatar for Pierre Lindenbaum
6 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

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

enter image description here

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Pierre Lindenbaum124k

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

ADD REPLYlink written 5 weeks ago by lucas.caue.jacintho30
1
gravatar for Vitis
4 weeks ago by
Vitis2.3k
New York
Vitis2.3k wrote:

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

ADD COMMENTlink written 4 weeks ago by Vitis2.3k
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