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Prerequisite files**\n-\n-| File type                                   | Source                                                                                                                  | Info                                                   | cisFusion/cisMuton        | cisCton                     |\n-| :--                                         | :--                                                                                                                     | :--                                                    | :--                       | :--                         |\n-| ${GROUP}.fasta (*1)                         | hg19 genome                                                                                                             | concatenate into single fasta in ascending order       | Required                  | Required                    |\n-| ${GROUP}.refGene.txt.gz                     | http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz                                                  | gz for cisFusion/cisMuton, gunzip for cisCton          | Required(refGene.txt.gz)  | Required(refGene.txt)       |\n-| ${GROUP}.geneName.txt.gz                    | http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/geneName.txt.gz                                                 |                                                        | Required                  | -                           |\n-| ${GROUP}.DBexome                            | http://www.genome.med.kyoto-u.ac.jp/SnpDB/HGVD1208-V1_41-dbSNP137.tar.gz                                                |                                                        | Required                  | -                           |\n-| ${GROUP}.snp.dbsnp                          | http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp138.txt.gz                                                   | gunzip and edit file extension `.txt` to `.snp.dbsnp`  | Required                  | -                           |\n-| ${GROUP}.genomicSuperDups.txt               | http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/genomicSuperDups.txt.gz                                         | gunzip                                                 | Required                  | -                           |\n-| ${GROUP}.rmsk                               | http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz                                                     | gunzip and remove file extension `.txt`                | Required                  | -                           |\n-| ${GROUP}.simpleRepeat                       | http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/simpleRepeat.txt.gz                                             | gunzip and remove file extension `.txt`                | Required                  | -                           |\n-| wgEncodeDukeMapabilityUniqueness20bp.bigWig | http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityUniqueness20bp.bigWig | converted from .bigWig                                 | -                         | Required                    |\n-| ${GROUP}.target.bed (*2)                    | bed file for capture region, depend on sample kit used                                                                  | prepare as `${GROUP}.bed` for cisCton.                 | Required                  | Required                    |\n-| ${GROUP}.fusion.bed (*3)                    | bed file for the definision of fusion region (it is also required for cisMuton)                                         | prepare as `target_fusion.txt` for cisCton             | Required                  | Required                    |\n-| ${GROUP}.gene.bed (*4)                      | bed file for capture region annotation                                                                                  |                                                        | Required                  | -                           |\n+| File type                                                          | Source                                                                                                                  | Info                                                                                                                                                     | cisFusion/cisMuton       | cisCton               |\n+| :--                                                                | :--                                                                                                                     | :--                                                                                                                                                      | :--                      | :--                   |\n+| `${GROUP}.fasta` (*1)                                              | hg19 genome                                                                                                             | concatenate into single fasta in ascending order                                                                                                         | Required                 | Required              |\n+| `${SAMPLE_NAME}.${GROUP}.fastq.R{1,2}.gz`                          |                                                                                                                         | sample file name which is going to be analyzed. (it could be single-end or bam file. change extentions in that case.)                                    | Required                 | -                     |\n+| `${BG_SAMPLE_NAME}.${GROUP}.fastq.R{1,2}.gz`                       |                                                                                                                         | normal(Back Ground) sample file name which is going to be used as negative control for calling mutation. extention could be modified as same above       | Required                 | -                     |\n+| `tmp/${SAMPLE_NAME}-RA.${GROUP}.MUTON.TARGET/common.fastq.aln.bam` |                                                                                                                         | bam file outputted by running cisMuton. some extension will be added to filename if you run by FFPE option. see [Copy Number Variation caller](./cton.md) section for more detail. | -                        | Required              |\n+| `${GROUP}.refGene.txt.gz`                                          | http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz                                                  | gz for cisFusion/cisMuton, gunzip for cisCton. You must subtract row so that all the gene listed in `${GROUP}.target.bed` will be included in here.      | Required(refGene.txt.gz) | Required(refGene.txt) |","path":"doc/INSTALL.md","position":57,"original_position":57,"commit_id":"f5139fd19aecbfc046868eec8bc0a0d3ec68b3ac","original_commit_id":"f5139fd19aecbfc046868eec8bc0a0d3ec68b3ac","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":"私が直します。\r\n","created_at":"2016-09-14T08:44:47Z","updated_at":"2016-09-14T08:44:47Z","html_url":"https://github.com/NCCJapan/cisCall5_doc/pull/6#discussion_r78708125","pull_request_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6","_links":{"self":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/comments/78708125"},"html":{"href":"https://github.com/NCCJapan/cisCall5_doc/pull/6#discussion_r78708125"},"pull_request":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6"}}},"pull_request":{"url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6","id":85165084,"html_url":"https://github.com/NCCJapan/cisCall5_doc/pull/6","diff_url":"https://github.com/NCCJapan/cisCall5_doc/pull/6.diff","patch_url":"https://github.com/NCCJapan/cisCall5_doc/pull/6.patch","issue_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/6","number":6,"state":"open","locked":false,"title":"explain why Muton has been run before Cton","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":"「Ctonを走らせる前にMutonを動かしてbamを準備すること」といった旨の説明を追記しました。","created_at":"2016-09-14T04:26:25Z","updated_at":"2016-09-14T08:44:47Z","closed_at":null,"merged_at":null,"merge_commit_sha":"35aa4e64099d6c1f156bc3aeef14ebec7c89c28f","assignee":{"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},"assignees":[{"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}],"milestone":null,"commits_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6/commits","review_comments_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6/comments","review_comment_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/comments{/number}","comments_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/6/comments","statuses_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/statuses/f5139fd19aecbfc046868eec8bc0a0d3ec68b3ac","head":{"label":"NCCJapan:update_cton_explanation","ref":"update_cton_explanation","sha":"f5139fd19aecbfc046868eec8bc0a0d3ec68b3ac","user":{"login":"NCCJapan","id":13513984,"avatar_url":"https://avatars.githubusercontent.com/u/13513984?v=3","gravatar_id":"","url":"https://api.github.com/users/NCCJapan","html_url":"https://github.com/NCCJapan","followers_url":"https://api.github.com/users/NCCJapan/followers","following_url":"https://api.github.com/users/NCCJapan/following{/other_user}","gists_url":"https://api.github.com/users/NCCJapan/gists{/gist_id}","starred_url":"https://api.github.com/users/NCCJapan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NCCJapan/subscriptions","organizations_url":"https://api.github.com/users/NCCJapan/orgs","repos_url":"https://api.github.com/users/NCCJapan/repos","events_url":"https://api.github.com/users/NCCJapan/events{/privacy}","received_events_url":"https://api.github.com/users/NCCJapan/received_events","type":"Organization","site_admin":false},"repo":{"id":66815704,"name":"cisCall5_doc","full_name":"NCCJapan/cisCall5_doc","owner":{"login":"NCCJapan","id":13513984,"avatar_url":"https://avatars.githubusercontent.com/u/13513984?v=3","gravatar_id":"","url":"https://api.github.com/users/NCCJapan","html_url":"https://github.com/NCCJapan","followers_url":"https://api.github.com/users/NCCJapan/followers","following_url":"https://api.github.com/users/NCCJapan/following{/other_user}","gists_url":"https://api.github.com/users/NCCJapan/gists{/gist_id}","starred_url":"https://api.github.com/users/NCCJapan/starred{/owner}{/repo}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