RepeatModeler - problem with creating library for RepeatMasker

Question

[loczi94]

Hi everyone!

I was trying to build library with RepeatModeler from fasta seqences (containing only transposons) of some species of fish. Let's say that I've done it, but I'm not sure if it's correct. My prepared fasta file contains 1072 sequences of fish, but the library created by RepeatModeler (file consensi.fa.classified) contains ONLY 8 sequences and I wonder if it isn't too less. Below I add exact command lines to show You what I've done, cause mabye I did something wrong through the process of creating the library. In addition to this, RepeatModeler didn't create .xdf file which I've expected after reading manual. Here's the link to example run: http://www.repeatmasker.org/RepeatModeler.html

Command lines: (Based on http://www.repeatmasker.org/RepeatModeler.html)

1. BuildDatabase -name Database -engine ncbi Mobile-elements.fasta
2. nohup RepeatModeler -engine ncbi -database Database >& run.out &

From manual:

-database The prefix name of a XDF formatted sequence database containing the genomic sequence to use when building repeat models. The database may be created with the WUBlast "xdformat" utility or with the RepeatModeler wrapper script "BuildXDFDatabase".

However there is no script like "BuildXDFDatabase" and WUBlast was replaced by AB-BLAST, which you have to pay for license.

I hope that someone can answer me, cause I doubt that this library is correct and i I can't go on with my project. Thanks in advance :)

Answer 1

[Philipp Bayer]

These 8 sequences aren't your total repeats, they are the type of repeat present in your genome, so if you run RepeatMasker with the classified output like

RepeatMasker -lib output.classified your_reference.fasta

you should see the "total" spread of repeats.

However, it looks like you used "Mobile-elements.fasta", I assume this doesn't contain your entire genome? Normally you run RepeatModeler with the entire genome, not with your repeat-candidates. You can compare that output with your Mobile-elements.fasta to see whether it fits, or run RepeatMasker directly with your Mobile-elements.fasta with the -lib flag.

The manual you have there is a bit old, so you did the right thing. You can't even get the "old" WU-BLAST anymore.