03-SoftmaskGenome.Rmd

# FixMe






####Softmask genome (RepeatMasker)

Link to the classified file in the dated directory that RepeatModeler makes
(my links didn’t work)

Softmask each in a separate directory first.
I did softmask in the dated directory that Repeat Modeler made for each  

Put whole path to RepeatMasker because I have a different miniconda:

```
/home/jm/sw/miniconda3/bin/RepeatMasker --help	

/home/jm/saved/Perlscripts/annotation/run-repeat-masker.bash
```


NOTE: BRAKER software:
https://github.com/Gaius-Augustus/BRAKER

UPDATE:

Template:

```
/home/jm/saved/Perlscripts/annotation/run-repeat-masker.bash <fasta> <fa.classified>
```

+ Input
    + <YourSeq.fasta>
    + <YourSeq.consensi.fa.classified>
    
+ Output
    + <YourSeq.consensi.fa.classified.gff>
    + <YourSeq.consensi.fa.classified.masked>
    + <YourSeq.consensi.fa.classified.?>
    + <YourSeq.consensi.fa.classified.?>


Code that worked:

```
/home/jm/saved/Perlscripts/annotation/run-repeat-masker.bash /data/fish/Annotation/Cbrontotheroides.fasta CbronConsensi.fa.classified
```

```
/home/jm/saved/Perlscripts/annotation/run-repeat-masker.bash /data/fish/Annotation/Cdesquamator.fasta CdesConsensi.fa.classified
```

```
/home/jm/saved/Perlscripts/annotation/run-repeat-masker.bash /data/fish/Annotation/Cvariegatus.fasta  CvarConsensi.fa.classified
```

run-repeat-masker.bash:

```
#! /usr/bin/bash
# Link to the *classified file in the dated directory it makes.
# Feed in the fasta file and the classified file
# repeat environment
#/home/jm/miniconda3/envs/repeat/bin/RepeatMasker
/home/jm/miniconda3/envs/repeat/bin/RepeatMasker -pa 16 -gff -nolow -lib $2 $1
```

+ pa - parallel, to use multiple processors

+ gff - creates an additional General Feature Finding format output (http://www.sanger.ac.uk/Software/GFF)

+ nolow - does not mask low complexity DNA or simple repeats, does not display simple repeats or low_complexity DNA in the annotation

+ lib - use the -lib option to specify a custom library of sequences to be masked in the query

Notes:

You can combine the repeats available in the RepeatMasker library  with a custom set of consensus sequences.  To accomplish this use the famdb.py tool:

```
`./famdb.py -i Libraries/RepeatMaskerLib.h5 families --format fasta_name --ancestors --descendants 'species name' --include-class-in-name`
```