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Old 06-06-2013, 06:13 PM   #1
BGould
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Default Can you explain this alignment coverage pattern?

Hello, I am visualizing RNA-seq PE reads using IGV and I see some strange but consistent patterns in the variation of depth of expression within some transcripts. I am aligning reads to a transcriptome that was assembled de novo. Is there a simple explanation for the pattern depicted in the attached image (see post directly below for image)? (There are two tracks, each representing a different individual.)

Is this alternative splicing? reads from two different paralogs aligning to the same transcript? an error in the construction of the original transcript in the denovo assembly that caused two different transcripts to merge?? If anyone out there has a lot of experience looking at these kind of alignments in RNA-seq data maybe it is obvious to you?
Many thanks!

Last edited by BGould; 06-06-2013 at 06:32 PM.
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Old 06-06-2013, 06:31 PM   #2
BGould
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Default Alignment Image attached

alignment image is attached here
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File Type: png Screen Shot 2013-06-06 at 10.01.45 PM.png (29.0 KB, 36 views)
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