Interpreting Color by Pair Orientation

[hou ri]

I have got several bam files using the same pipeline. However, the blue and aquamarine reads of two samples (A and B) cover the whole genomes.  

Has anyone encountered this issue earlier?

Best regards.

[igv-help]

IGV just displays the data in the BAM file and we (the IGV development team) can't comment on the data or its interpretation. Perhaps a more general forum, like SeqAnswers, can help with your question.

[igv-help]

Could you right-click over the A or B alignment track,  select "View as Pairs",  and show us the screenshot?

[hou ri]

Thank you for your message, and please accept my apologies for the delay in replying. 

Here I submit the screenshots after selecting "View as Pairs".

Best regards.

[igv-help]

There's something strange with your data,  there is no separation between the pairs, in most cases it looks like they nearly completely overlap.  This could indicate very short fragment sizes in you library,  but that is not my area of expertise.  You can see one "normal" looking pair for each sample,  towards the right, the pair mates are gray and facing each other, with a grey connecting line.

IGV is just showing what is in your file, we really can't speculate on what went wrong,  but it looks like it was library prep not alignment artifacts.   You might post a query to a more analysis or next gen focused forum.

[hou ri]

We find your comments to be highly valuable. Additionally, we believe there are issues with the library preparation.

Thank you very much.