Komal Rathi
I am looking at a specific location chr2:215595181-215595182 in RNAseq data and have a bunch of questions. I have colored the reads by insert size - see attached BARD1.png. I am not sure what the dark-red/wine color represents. I looked at the documentation but couldn't find an explanation for this particular color.
Q. Is it the same as the red color they show in the docs? If so does it represent deletions?
Q. When I hover over one of such colored reads, it shows read length as 101 bp and reference span as 1,501 bp (see attached read_and_reference_length.png). What does that mean?
Q. When I first uploaded the bam file to IGV, it showed me the colored reads (see Before_zooming_in.png). However, I zoomed in completely and zoomed out again the alignments changed and the color disappeared (see Zooming_in_and_out.png). I am so confused why the alignments and color changed when I just zoomed in and out of that particular region.
The two dashed black vertical lines represent chr2:215595181-215595182.
Thanks!!
