Mercurial > repos > petr-novak > dante_ltr

annotate README.md @ 6:b91ca438a1cb draft

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author petr-novak
date Thu, 19 May 2022 08:21:55 +0000
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1 # dante_ltr
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3 Tool for identification of complete LTR retrotransposons based on analysis of protein
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4 domains identified by DANTE tool.
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6 ## Installation:
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7
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8 ```shell
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9 conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr
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10 ```
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11 ## Usage
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12
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13 ```shell
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14 Usage: ./extract_putative_ltr.R COMMAND [OPTIONS]
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17 Options:
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18 -g GFF3, --gff3=GFF3
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19 gff3 with dante results
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21 -s REFERENCE_SEQUENCE, --reference_sequence=REFERENCE_SEQUENCE
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22 reference sequence as fasta
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24 -o OUTPUT, --output=OUTPUT
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25 output file path and prefix
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27 -c NUMBER, --cpu=NUMBER
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28 Number of cpu to use [default 5]
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30 -h, --help
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31 Show this help message and exit
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32 ```
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33
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34 ## Example
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35 ```shell
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36 mkdir -p tmp
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37 ./extract_putative_ltr.R -g test_data/sample_DANTE.gff3 -s test_data/sample_genome.fasta -o tmp/ltr_annotation
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38 ```
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40 ## Output files
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43 ### Output of script `extract_putative_ltr.R`:
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46 - `prefix.gff3` - annotation of all identified elements
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47 - `prefix_DL.fasta` - elements with protein **d**omains and **L**TR
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48 - `prefix_DLTP.fasta` - elements with **d**omains, **L**TR, **T**SD and **P**BS
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49 - `prefix_DLP.fasta` - elements with **d**omains, **L**TR and **P**BS
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50 - `prefix_DLT.fasta` - elements with **d**omains, **L**TR, **T**SD
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51 - `prefix_statistics.csv` - number of elements in individual categories