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Old 02-18-2017, 04:36 AM   #1
gen2prot
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Location: Hyderabad, India

Join Date: Apr 2010
Posts: 64
Default Cannot understand Repeatmasker behaviour

Hi All,

I used the MIPSRE-dat database to mask repeats in a maize BAC sequence using repeatmasker (default parameters). The repeatmasked file obtained, I gave as input to a custom built annotation pipeline, that I am testing and trying to improve. This pipeline has repeatmasker (RM) built in as a component. The run parameters for the pipeline RM is default again, and the database used is MIPSRE-dat again.

I was expecting that if a repeat masked file is run via repeatmasker again using the same database and run settings, I will not get additional repeat masking. However, that is not the case. I get additional repeatmasking in regions that was not repeat masked. i know this because the gff file that is obtained has coordinates not present in the first run.

I am confused about repeatmasker behavior. Can anyone please comment? What am i missing? Has anyone faced this before?

Thanks
Abhijit
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