How should a strand-specific experiment look like in IGV?

[Jim Robinson]

red = neg strand (first read of the pair is no the neg strand)
blue = pos strand
grey = pair information not available, so "first of pair" is undefined

[panos_ed]

Thanks Jim!

I selected "first-of-pair" as you told me but can't find out what the colors mean (and couldn't find it either in IGV's manual).

Can you please explain what the colors (red, blue and grey) mean?

[Jim Robinson]

Hi,

It depends on the library details, but you should could try "color by first-in-pair" from the popup menu. This will color by the strand of the template, rather than the read, at least for libraries I am familiar with. Also, igvtools has options to compute coverage by pair strand, although this isn't available in igv itself yet. Better strand support is on our radar.

Jim

[panos_ed]

I have a paired-end, strand-specific dataset and used Trinity to assemble the contigs. I then mapped the reads back to the contigs to calculate transcript abundance and viewed the resulting bam file in IGV (don't have a reference genome).

Is there a way that I can tell whether my dataset is really strand-specific just by looking at the picture in IGV? If I had single-end sequences I should expect to have reads only in one strand (i.e. pointing to the right). Am I right?

But since I have paired-end reads, what the IGV picture should look like?