Mercurial > repos > petr-novak > dante_ltr
annotate README.md @ 1:c1498f679b50 draft
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author | petr-novak |
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date | Wed, 09 Mar 2022 09:31:31 +0000 |
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1 # dante_ltr |
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2 |
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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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5 |
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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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15 |
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16 |
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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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20 |
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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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23 |
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24 -o OUTPUT, --output=OUTPUT |
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25 output file path and prefix |
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26 |
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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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29 |
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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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39 |
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40 ## Output files |
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41 |
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42 |
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43 ### Output of script `extract_putative_ltr.R`: |
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44 |
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45 |
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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 |