{"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":11,"created_at":"2018-08-23T11:03:22Z","updated_at":"2018-08-28T19:05:12Z","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/416704226","html_url":"https://github.com/churchill-lab/alntools/issues/2#issuecomment-416704226","issue_url":"https://api.github.com/repos/churchill-lab/alntools/issues/2","id":416704226,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNjcwNDIyNg==","user":{"login":"kbchoi-jax","id":7860891,"node_id":"MDQ6VXNlcjc4NjA4OTE=","avatar_url":"https://avatars1.githubusercontent.com/u/7860891?v=4","gravatar_id":"","url":"https://api.github.com/users/kbchoi-jax","html_url":"https://github.com/kbchoi-jax","followers_url":"https://api.github.com/users/kbchoi-jax/followers","following_url":"https://api.github.com/users/kbchoi-jax/following{/other_user}","gists_url":"https://api.github.com/users/kbchoi-jax/gists{/gist_id}","starred_url":"https://api.github.com/users/kbchoi-jax/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kbchoi-jax/subscriptions","organizations_url":"https://api.github.com/users/kbchoi-jax/orgs","repos_url":"https://api.github.com/users/kbchoi-jax/repos","events_url":"https://api.github.com/users/kbchoi-jax/events{/privacy}","received_events_url":"https://api.github.com/users/kbchoi-jax/received_events","type":"User","site_admin":false},"created_at":"2018-08-28T19:05:12Z","updated_at":"2018-08-28T19:05:12Z","author_association":"MEMBER","body":"That's an error from `bowtie`. Try `bowtie-build` directly using the transcriptome.fa file. [Here](http://bowtie-bio.sourceforge.net/manual.shtml#the-bowtie-build-indexer)'s the manual."}}
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