{"action":"created","comment":{"url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/comments/82359044","pull_request_review_id":3271917,"id":82359044,"diff_hunk":"@@ -75,19 +79,18 @@ See \"Prerequisite files\" in [installation of cisCall](./INSTALL.md) for input fi\n     - `tmp/${SAMPLE_NAME}.${GROUP}.MUTON.TARGET/common.*.bam`\n     - `tmp/${BG_SAMPLE_NAME}.${GROUP}.MUTON.TARGET/common.*.bam`.\n   - Bam file names are changed like `common.fastq.aln.bam` for frozen samples or `common.fastq.aln.none.bam.dup1331.bam` (or slightly different name) for FFPE samples according to the setting of cisMuton.\n-- *3<a name=\"note_grp\"> : `${GROUP}.bed` (=`${GROUP}.target.bed` for cisFusion/cisMuton) should be placed here. Only `${GROUP}` be set to this argument.\n \n ## <a name=\"analysis_type\">cisCton Analysis Type\n \n cisCton utilizes bam files generated by cisMuton. Therefore, cisCton analysis type should be set in accordance with the setting of cisMuton.\n \n | cisCton Analysis Type | Sample | Normal (backgroud) sample | Description                                      |\n | ---                   | ---    | ---                       | ---                                              |\n-| CTON                  | frozen | frozen ([*4](#note_bg))   | ([*5](#note_fr))                                 |\n-| CTON:DUP              | FFPE   | frozen ([*4](#note_bg))   | removing duplication (suitable for FFPE samples) |\n+| CTON                  | frozen | frozen ([*3](#note_bg))   | ([*4](#note_fr))                                 |\n+| CTON:DUP              | FFPE   | frozen ([*3](#note_bg))   | removing duplication (suitable for FFPE samples) |\n \n-- *4<a name=\"note_bg\"> : At the current version, cisCton is designed on the supposition that normal (background) samples are frozen.\n-- *5<a name=\"note_fr\"> : At the current version, cisCton has not been adjusted properly for frozen samples. So, please use cisCton for FFPE samples. \n+- *3<a name=\"note_bg\"> : At the current version, cisCton is designed on the supposition that normal (background) samples are frozen.","path":"doc/cton.md","position":57,"original_position":57,"commit_id":"475e84e622b39b584e2271672d0994c8c75e4b51","original_commit_id":"475e84e622b39b584e2271672d0994c8c75e4b51","user":{"login":"joemphilips","id":10084960,"avatar_url":"https://avatars.githubusercontent.com/u/10084960?v=3","gravatar_id":"","url":"https://api.github.com/users/joemphilips","html_url":"https://github.com/joemphilips","followers_url":"https://api.github.com/users/joemphilips/followers","following_url":"https://api.github.com/users/joemphilips/following{/other_user}","gists_url":"https://api.github.com/users/joemphilips/gists{/gist_id}","starred_url":"https://api.github.com/users/joemphilips/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/joemphilips/subscriptions","organizations_url":"https://api.github.com/users/joemphilips/orgs","repos_url":"https://api.github.com/users/joemphilips/repos","events_url":"https://api.github.com/users/joemphilips/events{/privacy}","received_events_url":"https://api.github.com/users/joemphilips/received_events","type":"User","site_admin":false},"body":"supposition は `assumption`　の方が自然です。","created_at":"2016-10-07T09:44:30Z","updated_at":"2016-10-07T09:44:30Z","html_url":"https://github.com/NCCJapan/cisCall5_doc/pull/19#discussion_r82359044","pull_request_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/19","_links":{"self":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/comments/82359044"},"html":{"href":"https://github.com/NCCJapan/cisCall5_doc/pull/19#discussion_r82359044"},"pull_request":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/19"}}},"pull_request":{"url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/19","id":88403467,"html_url":"https://github.com/NCCJapan/cisCall5_doc/pull/19","diff_url":"https://github.com/NCCJapan/cisCall5_doc/pull/19.diff","patch_url":"https://github.com/NCCJapan/cisCall5_doc/pull/19.patch","issue_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/19","number":19,"state":"open","locked":false,"title":"Additional minor changes for cisCton","user":{"login":"monagai","id":13533333,"avatar_url":"https://avatars.githubusercontent.com/u/13533333?v=3","gravatar_id":"","url":"https://api.github.com/users/monagai","html_url":"https://github.com/monagai","followers_url":"https://api.github.com/users/monagai/followers","following_url":"https://api.github.com/users/monagai/following{/other_user}","gists_url":"https://api.github.com/users/monagai/gists{/gist_id}","starred_url":"https://api.github.com/users/monagai/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/monagai/subscriptions","organizations_url":"https://api.github.com/users/monagai/orgs","repos_url":"https://api.github.com/users/monagai/repos","events_url":"https://api.github.com/users/monagai/events{/privacy}","received_events_url":"https://api.github.com/users/monagai/received_events","type":"User","site_admin":false},"body":"cisCton.mdの修正を行いました。(INSTALL.mdについてはこの後別ブランチで)\r\n- -nオプションの追加\r\n- 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