satMiner: A Toolkit to NGS satellite DNA mining and analysis
- 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
- BLAT http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/
- Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic
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.py NumberOfPairedReads LibraryA_1.fastq LibraryA_2.fastq MinQual MinLen
Run RepeatExplorer with default options.
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
UPDATE (July 2020): If you are using the RepeatExplorer2 version, please use rexp_get_contigs_re2.py instead.
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
$ deconseq_run.py ListOfFastqFiles Reference Threads
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.
$ rm_homology.py FastaFile
$ rm_getseq.py FastaFile RepeatMaskerOut [LenMinimum]
Optionally:
$ sat_cutter.py AlignedFastaFile
$ repeat_masker_run_big.py ListOfFastaFiles FastaReference NumberOfThreads
Pattern File with tab-separated names:
Sat-01A Sat-01A
Sat-02A Sat-02A
Sat-02B Sat-02A
Running script
$ sat_subfam2fam.py AlignFile PatternFile