repeat_analysis_pipeline_notes.txt

#Create Custom Repeat Library

export PATH=/usr/local/RepeatModeler:$PATH
BuildDatabase -name mim_repeat_lib_aug10 -engine ncbi M_aurantiacus_v1_single_ordered.fasta
RepeatModeler -database mim_repeat_lib_aug10 -pa 18

#Repeat Library: /home/afuiten/research/mimulus/august/RM_41342.FriAug121137132016/consensi.fa.classified

#Repeat Analysis

RepeatMasker -species "monkey flowers" -gff -pa 30 -a -xsmall M_aurantiacus_v1_splitline_ordered.fasta

#Output files:
M_aurantiacus_v1_splitline_ordered.fasta.masked     
M_aurantiacus_v1_splitline_ordered.fasta.cat.gz  
M_aurantiacus_v1_splitline_ordered.fasta.out.gff
M_aurantiacus_v1_splitline_ordered.fasta.align  
M_aurantiacus_v1_splitline_ordered.fasta.out     
M_aurantiacus_v1_splitline_ordered.fasta.tbl

RepeatMasker -lib /home/afuiten/research/mimulus/august/RM_41342.FriAug121137132016/consensi.fa.classified -gff -pa 30 -a -xsmall M_aurantiacus_v1_splitline_ordered.fasta.masked 

#Output files:

#Merge the *.out files from both runs:
cat M_aurantiacus_v1_splitline_ordered.fasta.out M_aurantiacus_v1_splitline_ordered.fasta.masked.out >> M_aurantiacus_v1_splitline_ordered.fasta.merged.out
M_aurantiacus_v1_splitline_ordered.fasta.merged.out

#Use the *.masked from the final run:
M_aurantiacus_v1_splitline_ordered.fasta.masked.masked

#Use the *.tbl from the final run:
M_aurantiacus_v1_splitline_ordered.fasta.masked.tbl

##Email to Robert Hubley regarding properly running RepeatMasker with a custom Library

Hi Dr. Hubley,

I am running RepeatMasker on my de novo genome assembly for a dicot plant using a custom repeat library I generated with RepeatModeler.
My commands are as follows:
RepeatMasker -lib plant_custom_liibrary.fa.classified -gff -pa 30 -a -xsmall plant_genome.fasta
When I open the .tbl summary file, I see that it reads "The query species was assumed to be homo ".
When I tried to add the -species flag to my RepeatMasker command, it says that "You can choose only one species option (including -species and -lib) at a time."
Is there a way to used both my custom repeat library and change the default species from Homo sapien?
If you could answer this question, I will be really grateful. I tried searching for this online and in the RepeatMasker documentation and I couldn't find a clear answer to my question.

Thank you,

Allison

##Response from Dr. Robert Hubley:

The "-lib" option is not additive.  
It does not first compare your sequence to the human library and then use the "-lib" library afterwards.  
It does use TRF and some low_complexity sequences stored in RepeatMaskerLib.embl to screen out these regions but does not search for TEs.  
You could achieve a similar result by first running RepeatMasker using the "-species" option on your sequence 
then follow that with a run on the *.masked file using your sequence library to pick up the elements missed in the standard libraries.  
You could then merge the *.out files from both runs and use the *.masked from the final run.

Let me know if you have any further questions,

-R