Clarification on Intron Retention Heatmap

[RacheliHadjez]

Hi,

First of all, thank you for developing and sharing this tool it's been very helpful!

I wanted to ask about the intron retention heatmap in the transcriptome_summary_plot.png output (from genemode). I'm having a hard time understanding what exactly is being shown in that part of the figure.

What do the red bars in the heatmap represent?

How is intron retention being quantified or summarized?

Is it normalized in any way?

I’ve looked at the documentation and the figure legend, but I’m still confused about how to interpret this section of the plot.

Also, I’m unsure how to interpret the x-axis in the plot: for example, when it says 1-2 transcripts per gene: does it include 2? or all the genes have only 1 transcript?

Thanks in advance for your help and clarification!

Best,
Rachel

[ammorse]

Hi Rachel

Each gene is only in one section of the plot so 6192 genes with exactly 1 transcript

1716 with 2/3
1055 with 4/5/6/7
394 with 8-15
16 with 16 to (max 51)

look at the block for the 1 transcript , since all the values for each gene will be 0 this is black because there is only 1 transcript

if you have 2 transcripts each gene could have a value of 0, .5 or 1 for the proportion of transcripts with an IR
for 3 transcripts values could be 0, 1/3 , 2/3 or 1

hope this helps and glad you like the tool!

Alison