RepeatMasker - differing results - help!

Question

[byrne.hazel1]

Hi all

I have an issue with repeatmasker that I can't figure out. When I perform two repeatmasker runs, one with the repbase library and one with a custom de novo library, around 10% more of the genome is masked versus combining these libraries in a fasta file and doing one run of repeatmasker.

Anyone experience anything similar?

[h.mon]

Did you edit your post? I think the previous version was better, as you described your problem in more detail. Or am I making some confusion here?

There are similar posts on the forum, but it will be very disappointing to you, because there are no answers in those posts:

Discrepencies between RepeatMasker searches with de-novo and repeatmasker libs

Differences Between Ucsc And Local Repeatmasker Results

[byrne.hazel1]

Thanks for the reply! I edited it as I thought it was too long and perhaps people weren't reading it all - if someone replied with something useful I could give more information again.

Thank you for these links - I had scoured this forum and seqanswers before posting and couldn't find any relevant answers unfortunately