RepeatMasker - differing results - help!
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?
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byrne.hazel1 •
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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
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