TEmin

Iterative protocol for the analysis of repetitive elements in non model organisms

Installation

• Copy script to your binaries folder.
• Dependencies:
  • BioPython http://biopython.org/wiki/Main_Page
  • RepeatMasker http://www.repeatmasker.org/RMDownload.html
  • seqTK https://github.com/lh3/seqtk
  • DeconSeq http://deconseq.sourceforge.net
  • Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic
  • dnaPipeTE https://github.com/clemgoub/dnaPipeTE

1. Repetitive elements mining (from the satMiner pipeline https://github.com/fjruizruano/satminer)

1a. Preparing sequences to RepeatExplorer

There is not a number of paired reads to start. You can try with 100000 or 200000. You should also indicate the minimum quality and the minimum length. For example if you are using Illumina PE 2x100 reads, you can try 20 and 100, respectively.

$ rexp_prepare_normaltag.py NumberOfPairedReads LibraryA_1.fastq LibraryA_2.fastq MinQual MinLen

1b. Run RepeatExplorer

Run RepeatExplorer with default options.

1c. Get contigs

Uncompress RepeatExplorer's output and go to the "clusters" folder. Get a list with the name of the contigs representing a half of the number of the cluster reads reads.

$ cd seqClust/clustering/clusters
$ rexp_get_contigs.py

Since clusters with few number of reads are difficult to distinguish as satDNA clusters, we select a half of the clusters and we then extract the sequences as a FASTA file:

$ extract_seq.py FastaFile List

1d. Run DeconSeq

$ deconseq_run.py ListOfFastaFiles Reference Threads

1e. Prepare filtered reads to RepeatExplorer

Usually, we recommend to duplicate the number of reads.

$ rexp_prepare_deconseq.py NumberOfPairedReads LibraryA_clean_1.fastq LibraryA_clean_2.fastq

You will then get a FASTA file to run again RepeatExplorer, so continue with step 1b.

1f. Annotate RepeatExplorer contigs

Annotation file:

CL1	DNA/hAT
CL2	DNA/Sola1
CL3	LTR/Copia-SIRE
CL4	LINE
CL5	LTR/Gypsy-TatRetand
CL6
CL7	LTR/Gypsy-Tat

Transfer annotation from annotation file to RepeateExplorer Contigs

$ rexp_annot.py RexpFastaFile AnnotationFile [Unknown]

2. Launch dnaPipeTE and annotate contigs

Launch dnaPipeTE:

$ python3 /directory/to/dnaPipeTE.py -input directory/to/reads_1.fastq -output /output/directory/ -cpu 12 -sample_number 2 -sample_size 500000 -RM_lib /directory/to/database.fasta -Trin_glue 10 -contig_length 300

Remove "Low_complexity", "Simple_repeat" and "Unknown" annotations:

$ cd /directory/to/dnapipete/run/Annotation/
$ grep -v "Low_complexity" one_RM_hit_per_Trinity_contigs | grep -v "Simple_repeat" | grep -v "Unknown" > one_RM_hit_per_Trinity_contigs_mod

Annotate contigs:

$ dnapipete_createdb.py ../Trinity.fasta one_RM_hit_per_Trinity_contigs_mod

3. Abundance and divergence

Generate repeat landscapes in a selection of reads in FASTA format:

$ repeat_masker_run_big.py ListOfFastaFiles FastaReference NumberOfThreads

To test purposes:

$ divsum_join_annot.py RepeatLandscapeFile AnnotationFile