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cbase [2017/10/12 13:07]
dweghorn
cbase [2017/10/12 14:31]
dweghorn
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 ===== Download ===== ===== Download =====
 +
 +{{ :​cbase_v1.0.gzip | CBaSE v1.0 }}
  
 ===== Usage ===== ===== Usage =====
 +
 +=== Running CBaSE ===
  
 <​code>​ <​code>​
 python ​ python ​
 </​code>​ </​code>​
 +
 +=== Input file format ===
 +
 +^Gene symbol^Mutation effect ​      ​^Mutated nucleotide ​      ​^Context index^
 +|ECE1 |coding-synon |C |38|
 +|SAMD11 |missense |A |29|
 +|TNFRSF4 |nonsense |A |28|
 +
 +
 +(1) Gene name
 +    Corresponds to the official gene symbol as used in the UCSC knownGene track.
 +(2) Mutation effect
 +    One of ["​missense",​ "​nonsense",​ "​coding-synon",​ "​intron",​ "​utr-3",​ "​utr-5",​ "​IGR"​] ("​intron"​ and "​IGR"​ mutations are discarded).
 +(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 tool =====
  
 You can also find a web-based user interface for CBaSE here: http://​genetics.bwh.harvard.edu/​cbase/​index.html You can also find a web-based user interface for CBaSE here: http://​genetics.bwh.harvard.edu/​cbase/​index.html