repeatmasker

I installed repeatmasker locally in my bin directory: /uufs/chpc.utah.edu/common/home/u6007910/bin/RepeatMasker/ (http://www.repeatmasker.org/RMDownload.html). I used HMMER and Dfam as the default sequence search engine for repeatmasker.

To install:

perl configure

This will prompt for various paths, most specific ones are as follows:

• 1. I had to specify the path for TRF.pm, which is present in the RepeatMasker folder: /uufs/chpc.utah.edu/common/home/u6007910/bin/RepeatMasker

  2. I had to specify the path for HMMER nhmmer program which is installed globally on the cluster: /uufs/chpc.utah.edu/sys/installdir/hmmer3/3.1b2/bin

  3. I had to specify the path for Dfam.hmm which is present in the RepeatMasker/Libraries folder (or can be downloaded): /uufs/chpc.utah.edu/common/home/u6007910/bin/RepeatMasker/Libraries

Once, the program is installed, you can test run to get the help options: ./RepeatMasker -h

FILTERING ON SEPT 27, 2018

makeblastdb -in /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/matt_transcriptome/txome_assembly/trinity_denovo/trinity_out_dir/bowtieassembly/Trinity.fasta -dbtype nucl

makeblastdb -in trinitydenovo.no_tes.fa -dbtype nucl

makeblastdb -in /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/dovetail_melissa_genome/Annotation/repeatmodeller/RM_108478.FriJul201433492018/consensi.fa.classified -dbtype nucl

perl fastaqual_select.pl -f /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/dovetail_melissa_genome/Annotation/repeatmodeller/RM_108478.FriJul201433492018/consensi.fa.classified -e <(awk '{print $1}' repeatmodlib_transcriptsnotes_blastn.out | sort | uniq) > repeatmodellib.no_prots.fa

perl fastaqual_select.pl -f trinitydenovo.no_tes.fa -e <(awk '{print $1}' repeatmodlibdb_transcriptsnotes_blastn.out | sort | uniq) > repeatmodellibdb.no_tes.fa

##numbers

646092 Trinity.fasta

2820 repeatmasklib_transcripts_blastn.out #blast transcriptome against repeatmasker repeat library

641980 trinitydenovo.no_tes.fa #removed the hits from the transcriptome

646092 Trinity.fasta

641980 trinitydenovo.no_tes.fa

280782 repeatmodlibdb_transcriptsnotes_blastn.out #blast transcriptome with no repeatmasker hits (From above) with the repeatmodeler library

401256 repeatmodellibdb.no_tes.fa #removed the hits from the trinitydenovo.no_tes.fa transcriptome

#blast repeatmodeler library against the transcriptome no tes file

7507 repeatmodlib_transcriptsnotes_blastn.out

#repeats in the transcriptome

196 repeatmodellib.no_prots.fa

### blasting transcriptome against repeatmodeler library

646092 Trinity.fasta

283412 repeatmodlib_transcripts_blastn.out #blast transcriptome againts repeatmodeler library

402974 trinitydenovo_repeatmod.no_tes.fa #removed hits from the transcriptome

7501 repeatmodlib.no_prots.fa #blast repeatmod library against transcriptome to get TEs

perl fastaqual_select.pl -f /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/matt_transcriptome/txome_assembly/trinity_denovo/trinity_out_dir/bowtieassembly/Trinity.fasta -e <(awk '{print $1}' repeatmodlib_transcripts_blastn.out | sort | uniq) > trinitydenovo_repeatmod.no_tes.fa