FAQ#467 Version1
Version 1/1 - Current version
What are Entry Points?
| Category: | Getting Started with Genboree | Difficluty: |  |
| Assigned to: | - | Due date: | |
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Answer
What are Entry Points?¶
- Entry points comprise the coordinate system on which annotations are made.
- For example, a chromosome is an entry point. For unassembled genomes, the scaffolds might be the entry points.
- Entry points must be defined within Genboree, with a name and a length, so that annotations can be placed on them.
- Currently, entry points are independent within Genboree; i.e. not directly linked. They are simply the names of chromosomes
- Entry points can be uploaded in two different formats:
- 3-column LFF
- The entry point name
- The keyword "Chromosome"
- The length of the entry point
- Fasta files
- 3-column LFF
- http://www.genboree.org/java-bin/showHelp.jsp?topic=definingAGenome#whatAreEPs
- http://www.genboree.org/java-bin/showHelp.jsp?topic=uploadEPhowto
Real Example¶
As an example, you can download the chromosome sizes for Mouse MM10 from UCSC:We can turn this into a 3 column LFF format for uploading onto Genboree with some very light formatting:
chr1 Chromosome 195471971 chr2 Chromosome 182113224 chrX Chromosome 171031299 chr3 Chromosome 160039680 chr4 Chromosome 156508116 chr5 Chromosome 151834684 chr6 Chromosome 149736546 chr7 Chromosome 145441459 chr10 Chromosome 130694993 chr8 Chromosome 129401213 chr14 Chromosome 124902244 chr9 Chromosome 124595110 chr11 Chromosome 122082543 chr13 Chromosome 120421639 chr12 Chromosome 120129022 chr15 Chromosome 104043685 chr16 Chromosome 98207768 chr17 Chromosome 94987271 chrY Chromosome 91744698 chr18 Chromosome 90702639 chr19 Chromosome 61431566 chr5_JH584299_random Chromosome 953012 chrX_GL456233_random Chromosome 336933 chrY_JH584301_random Chromosome 259875 chr1_GL456211_random Chromosome 241735 chr4_GL456350_random Chromosome 227966 chr4_JH584293_random Chromosome 207968 chr1_GL456221_random Chromosome 206961 chr5_JH584297_random Chromosome 205776 chr5_JH584296_random Chromosome 199368 chr5_GL456354_random Chromosome 195993 chr4_JH584294_random Chromosome 191905 chr5_JH584298_random Chromosome 184189 chrY_JH584300_random Chromosome 182347 chr7_GL456219_random Chromosome 175968 chr1_GL456210_random Chromosome 169725 chrY_JH584303_random Chromosome 158099 chrY_JH584302_random Chromosome 155838 chr1_GL456212_random Chromosome 153618 chrUn_JH584304 Chromosome 114452 chrUn_GL456379 Chromosome 72385 chr4_GL456216_random Chromosome 66673 chrUn_GL456393 Chromosome 55711 chrUn_GL456366 Chromosome 47073 chrUn_GL456367 Chromosome 42057 chrUn_GL456239 Chromosome 40056 chr1_GL456213_random Chromosome 39340 chrUn_GL456383 Chromosome 38659 chrUn_GL456385 Chromosome 35240 chrUn_GL456360 Chromosome 31704 chrUn_GL456378 Chromosome 31602 chrUn_GL456389 Chromosome 28772 chrUn_GL456372 Chromosome 28664 chrUn_GL456370 Chromosome 26764 chrUn_GL456381 Chromosome 25871 chrUn_GL456387 Chromosome 24685 chrUn_GL456390 Chromosome 24668 chrUn_GL456394 Chromosome 24323 chrUn_GL456392 Chromosome 23629 chrUn_GL456382 Chromosome 23158 chrUn_GL456359 Chromosome 22974 chrUn_GL456396 Chromosome 21240 chrUn_GL456368 Chromosome 20208 chrM Chromosome 16299 chr4_JH584292_random Chromosome 14945 chr4_JH584295_random Chromosome 1976