Tophat fusion : visualize results

[NicoBxl]

Hi,

After the execution of tophat-fusion. I want to visualize the alignment in IGV. So with the sam output file I execute samtools to convert it in a bam file :

So :

samtools view -bS -o M267_T0_fusion.bam accepted_hits.sam

It gives me this error :

[samopen] SAM header is present: 28 sequences.
[sam_read1] reference 'HSA4-HSA20' is recognized as '*'.
Parse error at line 133: invalid CIGAR operation
[bam_header_read] EOF marker is absent. The input is probably truncated.
Anyone has an idea on how resolve this error ?

Thanks,

N.

[Nicolas]

The authors explained on their website that they introduced the CIGAR F, for fusion, but the consequence is that it breaks the possibility to convert into BAM.

http://tophat-fusion.sourceforge.net/manual.html#output

How would you like to visualise in IGV when you have a read mapping to 2 chromosomes? Is that possible in IGV?

[bharati]

tophat fusion post output

Can you please explain tophat fusion post output ie result.html file

[bharati]

Confusion between Spanning reads and spanning mate pairs

Hi NicoBxl

Can you please explain the difference between Spanning Reads and Spanning Mate pairs. As much I could understand Spanning reads are those reads which do not harbor the fusion point but Split reads do harbor it, but Spanning mate pairs are those spanning reads which are supported by their mate pairs and the number of Spanning mate pairs should be lesser than spanning reads, but this is not the case in my results.