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jyhehir / mobster

For more details about Mobster please see
https://jyhehir.github.io/mobster/index.html
GNU General Public License v3.0
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Chromosomal mapping issue #44

Closed kaanokay closed 3 years ago

kaanokay commented 3 years ago

Hi,

When I completed transposable calling using Mobster, realized that several samples with female gender had chromosome Y-mapped transposable insertions. As you know, it's not impossible but very rare. In addition to Mobster, I used a different transposable caller tool but encountered the same issue.

Did you encounter such a situation like mine before?

I am wondering the reason for that. Do you have any comments on my situation?

Best wishes.

jyhehir commented 3 years ago

Hi, The first thing that pops into my mind is the pseudo autosomal regions on chrX have a prediction, which then duplicates itself due to multi mapping on chrY. Do you see anything in the data which might support that concept?

Regards, Jayne

kaanokay commented 3 years ago

@jyhehir ,

Thanks for your reply. I explored it. Chromosomal-assignment of specific insertions is based on reference-genome (it could be female or male). Another reason for that is related to pseudo-autosomal regions as you estimated. I took answers and am convinced.

Thanks for your help.

Best.