Jeb Rosen

It is difficult to answer this question for certain. RepeatModeler uses several different strategies - including RepeatScout, RECON, and optionally LTR_Retriever - to search for possible repetitive elements in samples...

Can you show the output of `ls -l /home/brittany/Aaron/RepeatMasker/Polycephalomyces_Cleaned.fasta`? --- It looks like you are using only Dfam. Dfam does not include any fungal-specific repeats, so the masking will likely...

That is very unusual: the `Polycephalomyces_Cleaned.fasta` file is not readable or writable by anyone. Running the command `chmod 0644 Polycephalomyces_Cleaned.fasta` will reset it to a sane default, and after that...

Hi! I think some of your question about `lib` and `species` has been answered before: . Does this help? EMBL contains the same information as FASTA and more, so converting...

> Is that ok? This is a difficult question because it depends on your particular project or goals. The answer I linked before suggests two separate RepeatMasker runs: one with...

I am not sure I understand your question. You could use the family models from RepeatModeler for a second round of masking with `-lib` as I described above, if you...

You can use `util/queryRepeatDatabase.pl` in the `-tree` mode to view all of the species and number of repeat families that are covered by your configured libraries. It is possible that...

@xiaoyezao are you using a version of Dfam and/or RepBase that has repeats for the species you ran RepeatMasker on? > You can use `util/queryRepeatDatabase.pl` in the `-tree` mode to...

@aditi17142 > The assumed RepeatMasker installation directory > /home/guest1/maker/RepeatMasker > does not appear to be correct Did you install RepeatMasker in the directory named `/home/guest1/maker/RepeatMasker`, or was RepeatMasker installed automatically...

> I would like to mention that both the folders Libraries and Matrices are present within the folder where RepeatMasker is installed. > Still the error is showing up. What...