IGV-results of Bowtie mapping, strange colors!

Question

[ann-katrin.buch]

Dear all,

i am having trouble interpreting the IGV-results i got after Bowtie2-mapping. The colors that are showing up are looking very different from the ones they use in their manual. As you can see in the uploaded picture there is lots of dark red, really lots of them but with good mapping quality. Also there are lots of white bars, indicating a mapping quality of 0 if i am right. I strongly doubt my gene of interest has that many deletions(which would be one explanation according to the manual)! I already asked our bioinformatition who also did the plotting for me but since we both could not find an explanation i decided to ask someone, thats what i am doing right now :)

I would be very happy if someone could help me and provide me some insight into this gaphic so i could actually interprete it!

Thanks a lot and best wishes,

Ann-Katrin!

IGV-result

[Devon Ryan]

Your IGV link is wrong and there's no apparent way for us to fix it.

[GenoMax]

I fixed the link for the image. @ann-katrin confirm that the image is the right one.

[Devon Ryan]

Your URL parsing skills are better than mine :)

[GenoMax]

Not really. Just got lucky :-)

[GenoMax]

Is the correct reference genome loaded in IGV? That seems to catch people off-guard easily. Did the alignment stat look reasonable (independent of IGV)?

Answer 1

[skbrimer]

I'm not 100% on this since I don't do human work but it looks like you have mate pairs where one pair is on your area of interest and the other is on a different chromosome.

If you don't get an answer here I would recommend reaching out to Broad and asking them. They are pretty good about getting back to people.

Good Luck.

[GenoMax]

This appears to be some sort of de novo assembly (B pertusis)?

[skbrimer]

hmmm.... good point.

In the documentation they only place it lists those colors are in the inter-chromosomal rearrangement section. http://www.broadinstitute.org/igv/interpreting_insert_size

[GenoMax]

That may still be applicable here with the scaffolds being treated as chromosomes. This could be a case of the assembly not being of good quality.