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Output
Lorraine Ayad edited this page Jan 24, 2018
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The CNEs output will be in BED format as follows:
chr2 144146055 144146220 chr7 32701448 32701613 165 165 95.15
chr2 144149385 144149598 chr7 32704280 32704495 213 215 95.31
chr2 144388596 144388788 chr7 32811411 32811604 192 193 96.35
chr2 144397232 144397433 chr7 32821983 32822184 201 201 95.02
chr2 144402300 144402477 chr7 32827696 32827873 177 177 95.48
chr2 144402500 144402666 chr7 32827896 32828061 166 165 95.15
chr2 144403589 144403824 chr7 32829025 32829260 235 235 98.30
chr2 144427145 144427551 chr7 32839564 32839966 406 402 95.02
Column 1: Chromosome name in the reference genome.
Column 2: The start coordinate of the CNE in the specified chromosome of the reference genome.
Column 3: The end coordinate of the CNE in the specified chromosome of the reference genome.
Column 4: Chromosome name in the query genome.
Column 5: The start coordinate of the CNE in the specified chromosome of the query genome.
Column 6: The end coordinate of the CNE in the specified chromosome of the query genome.
Column 7: Length of CNE in reference sequence.
Column 8: Length of CNE in query sequence.
Column 9: Similarity threshold of CNE.
The above example is the truncated output of the following command
./cnef -r hg38.fa -q galGal4.fa -e hg38_exons -f galGal4_exons -y 2 -z 7 -a 144121063 -b 146282147 -c 31812269 -d 33916777 -t 0.95 -l 150 -o output