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lines changed Original file line number Diff line number Diff line change @@ -59,11 +59,11 @@ such as the library **nrTEplants**. The script does not load the resulting annot
5959./AnnotRedRepeats.py ../files/nrTEplantsJune2020.fna test_Atha_chr4 --bed_file test.bed
6060
6161# consider only repeats with length >= 200 bp
62- ./AnnotRedRepeats.py files/nrTEplantsJune2020.fna Brachypodium_distachyon --cor 4 \
62+ ./AnnotRedRepeats.py ../ files/nrTEplantsJune2020.fna Brachypodium_distachyon --cor 4 \
6363 --minlen 200
6464
6565# add annotated repeats to Ensembl core db and use a different minimap2 binary
66- ./AnnotRedRepeats.py files/nrTEplantsJune2020.fna Brachypodium_distachyon --exe /path/to/minimap2 --cor 4 \
66+ ./AnnotRedRepeats.py ../ files/nrTEplantsJune2020.fna Brachypodium_distachyon --exe /path/to/minimap2 --cor 4 \
6767 --host pl1 --user xyz --pw XYZ \
6868 --port 123 --db brachypodium_distachyon_core_49_102
6969```
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