{"__v":0,"_id":"5797b918209a6e0e00b8321c","category":{"__v":0,"_id":"5797b8e5209a6e0e00b8321b","project":"57618347b65324200072d6a5","version":"57618347b65324200072d6a8","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-07-26T19:24:21.598Z","from_sync":false,"order":1,"slug":"test-1","title":"FAQ"},"parentDoc":null,"project":"57618347b65324200072d6a5","user":"57617c8caa540f3600bfed20","version":{"__v":8,"_id":"57618347b65324200072d6a8","project":"57618347b65324200072d6a5","createdAt":"2016-06-15T16:33:11.587Z","releaseDate":"2016-06-15T16:33:11.587Z","categories":["57618347b65324200072d6a9","5761912d207db7170022fbe9","57619455a7c9f729009a74e0","576e8ae1f37ab41700147471","5797b8e5209a6e0e00b8321b","57989a8817ced017003c4c69","579ca6f3d46f960e0029a8ec","579ca703fefb1d0e00c94f06"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"blobtools v0.9.19","version_clean":"0.9.19","version":"0.9.19"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-07-26T19:25:12.198Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"### How do I add a program to my $PATH variable?\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"$ export PATH=\\\"/path/to/samtools:$PATH\\\"\",\n      \"language\": \"shell\"\n    }\n  ]\n}\n[/block]\n### The taxonomies for the sequences that blobtools inferred are not what I expected. Why? \n\nBlobtools takes the information from hits files and essentially just sums up bitscores by taxonomic group at each taxonomic rank (see [taxonomy](doc:taxonomy) and [tax-rule](doc:tax-rule)). It does not do anything clever.\n\nReasons for not arriving at the correct taxonomy:\n* Number of spurious hits is greater than number of good hits: \n  * Imagine a sequence similarity search yielded the following result: \n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"taxonomic group\",\n    \"h-1\": \"score\",\n    \"h-2\": \"\",\n    \"0-0\": \"A\",\n    \"0-1\": \"300\",\n    \"1-0\": \"B\",\n    \"1-1\": \"110\",\n    \"2-0\": \"B\",\n    \"2-1\": \"108\",\n    \"3-0\": \"B\",\n    \"3-1\": \"101\"\n  },\n  \"cols\": 2,\n  \"rows\": 4\n}\n[/block]\nAlthough the best hit is to A, the taxonomy for that sequence would be set to B (score-sum = 319).","excerpt":"","slug":"frequently-asked-questions","type":"basic","title":"Frequently Asked Questions"}

Frequently Asked Questions


### How do I add a program to my $PATH variable? [block:code] { "codes": [ { "code": "$ export PATH=\"/path/to/samtools:$PATH\"", "language": "shell" } ] } [/block] ### The taxonomies for the sequences that blobtools inferred are not what I expected. Why? Blobtools takes the information from hits files and essentially just sums up bitscores by taxonomic group at each taxonomic rank (see [taxonomy](doc:taxonomy) and [tax-rule](doc:tax-rule)). It does not do anything clever. Reasons for not arriving at the correct taxonomy: * Number of spurious hits is greater than number of good hits: * Imagine a sequence similarity search yielded the following result: [block:parameters] { "data": { "h-0": "taxonomic group", "h-1": "score", "h-2": "", "0-0": "A", "0-1": "300", "1-0": "B", "1-1": "110", "2-0": "B", "2-1": "108", "3-0": "B", "3-1": "101" }, "cols": 2, "rows": 4 } [/block] Although the best hit is to A, the taxonomy for that sequence would be set to B (score-sum = 319).