{"action":"created","issue":{"url":"https://api.github.com/repos/churchill-lab/alntools/issues/2","repository_url":"https://api.github.com/repos/churchill-lab/alntools","labels_url":"https://api.github.com/repos/churchill-lab/alntools/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/churchill-lab/alntools/issues/2/comments","events_url":"https://api.github.com/repos/churchill-lab/alntools/issues/2/events","html_url":"https://github.com/churchill-lab/alntools/issues/2","id":353331097,"node_id":"MDU6SXNzdWUzNTMzMzEwOTc=","number":2,"title":"Preparation of sparse compressed incidence matrix","user":{"login":"mfrancesconi81","id":26404231,"node_id":"MDQ6VXNlcjI2NDA0MjMx","avatar_url":"https://avatars3.githubusercontent.com/u/26404231?v=4","gravatar_id":"","url":"https://api.github.com/users/mfrancesconi81","html_url":"https://github.com/mfrancesconi81","followers_url":"https://api.github.com/users/mfrancesconi81/followers","following_url":"https://api.github.com/users/mfrancesconi81/following{/other_user}","gists_url":"https://api.github.com/users/mfrancesconi81/gists{/gist_id}","starred_url":"https://api.github.com/users/mfrancesconi81/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mfrancesconi81/subscriptions","organizations_url":"https://api.github.com/users/mfrancesconi81/orgs","repos_url":"https://api.github.com/users/mfrancesconi81/repos","events_url":"https://api.github.com/users/mfrancesconi81/events{/privacy}","received_events_url":"https://api.github.com/users/mfrancesconi81/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-08-23T11:03:22Z","updated_at":"2018-08-24T17:00:44Z","closed_at":null,"author_association":"NONE","body":"Hi, \r\n\r\nI'm trying to perform ASE using EMASE. I am trying to follow the documentation of alntools to produce the sparse alignment incident matrix, but I am not quite sure on the details of the diploid BAM alignment to input in alntools.  Does it has to be an alignment to diploid transcriptome? or genome? Which aligner should I use? How should I prepare the reference diploid genome/transcriptome? Should I only output the best alignment? \r\n\r\nMany thanks, \r\n\r\nMirko"},"comment":{"url":"https://api.github.com/repos/churchill-lab/alntools/issues/comments/415819793","html_url":"https://github.com/churchill-lab/alntools/issues/2#issuecomment-415819793","issue_url":"https://api.github.com/repos/churchill-lab/alntools/issues/2","id":415819793,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNTgxOTc5Mw==","user":{"login":"mfrancesconi81","id":26404231,"node_id":"MDQ6VXNlcjI2NDA0MjMx","avatar_url":"https://avatars3.githubusercontent.com/u/26404231?v=4","gravatar_id":"","url":"https://api.github.com/users/mfrancesconi81","html_url":"https://github.com/mfrancesconi81","followers_url":"https://api.github.com/users/mfrancesconi81/followers","following_url":"https://api.github.com/users/mfrancesconi81/following{/other_user}","gists_url":"https://api.github.com/users/mfrancesconi81/gists{/gist_id}","starred_url":"https://api.github.com/users/mfrancesconi81/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mfrancesconi81/subscriptions","organizations_url":"https://api.github.com/users/mfrancesconi81/orgs","repos_url":"https://api.github.com/users/mfrancesconi81/repos","events_url":"https://api.github.com/users/mfrancesconi81/events{/privacy}","received_events_url":"https://api.github.com/users/mfrancesconi81/received_events","type":"User","site_admin":false},"created_at":"2018-08-24T17:00:44Z","updated_at":"2018-08-24T17:00:44Z","author_association":"NONE","body":"Hi Narayanan,\n\nWhich command of g2gtools should I use for this purpose?\n\nThanks,\n\nM.\n\nOn Fri, 24 Aug 2018 at 12:57, Narayanan Raghupathy <notifications@github.com>\nwrote:\n\n> The maternal and paternal transcriptomes should have unique IDs. For\n> example, if we use ensembl annotation, we label maternal allele as\n> ENSG001_M and paternal allele as ENSG001_P. That way we know the\n> chromosomal location from ensembl ID and haplotypic origin from M/P tag.\n> g2gtools can create these diploid transcriptome with user specified tags.\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/churchill-lab/alntools/issues/2#issuecomment-415725781>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AZLlh-3eWr2UEeBz7s9XTabI5yqa0mt2ks5uT9wtgaJpZM4WJTlQ>\n> .\n>\n"}}
{"actor":{"display_login":"mfrancesconi81"}}