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cbase [2017/10/12 17:42]
cbase [2017/10/29 22:22] (current)
Line 17: Line 17:
 ^Gene symbol^Mutation effect ​      ​^Mutated nucleotide ​      ​^Context index^ ^Gene symbol^Mutation effect ​      ​^Mutated nucleotide ​      ​^Context index^
-|ECE1 |coding-synon |C |38+|ECE1 |coding-synon |C |26
-|SAMD11 |missense |A |29+|SAMD11 |missense |A |53
-|TNFRSF4 |nonsense |A |28|+|TNFRSF4 |nonsense |A |52|
-(1) Gene symbol +(1) **Gene symbol** -- corresponds ​to the official gene symbol as used in the UCSC knownGene track.\\ 
-    Corresponds ​to the official gene symbol as used in the UCSC knownGene track. +(2) **Mutation effect** -- one of ["​missense",​ "​nonsense",​ "​coding-synon",​ "​utr-3",​ "​utr-5"​].\\ 
-(2) Mutation effect +(3) **Mutated nucleotide** -- one of [A, C, G, T].\\ 
-    One of ["​missense",​ "​nonsense",​ "​coding-synon", "​intron", "​utr-3",​ "utr-5", "IGR"​] ​("​intron"​ and "​IGR"​ mutations are discarded)+(4) **Context index** -- 0-based indices of tri- or pentanucleotide ​contexts can be looked up [[pagename|here]].
-(3) Mutated nucleotide +
-    One of [A, C, G, T]. +
-(4) Context index +
-    ​0-based indices of trinucleotide ​contexts can be looked up here.+
-===== CBaSE tool =====+===== CBaSE web tool =====
-You can also find a web-based user interface for CBaSE here: http://​genetics.bwh.harvard.edu/​cbase/​index.html+The CBaSE web tool can be found [[http://​genetics.bwh.harvard.edu/​cbase/​index.html|here]]. 
 +===== How to cite ===== 
 +Please cite 
 +Contact: [[dweghorn@research.bwh.harvard.edu|Donate Weghorn]]