{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/269","repository_url":"https://api.github.com/repos/COMBINE-lab/salmon","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/269/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/269/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/269/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/269","id":351033988,"node_id":"MDU6SXNzdWUzNTEwMzM5ODg=","number":269,"title":"Alevin: Adding support for CEL-Seq","user":{"login":"PeteHaitch","id":1049741,"node_id":"MDQ6VXNlcjEwNDk3NDE=","avatar_url":"https://avatars0.githubusercontent.com/u/1049741?v=4","gravatar_id":"","url":"https://api.github.com/users/PeteHaitch","html_url":"https://github.com/PeteHaitch","followers_url":"https://api.github.com/users/PeteHaitch/followers","following_url":"https://api.github.com/users/PeteHaitch/following{/other_user}","gists_url":"https://api.github.com/users/PeteHaitch/gists{/gist_id}","starred_url":"https://api.github.com/users/PeteHaitch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PeteHaitch/subscriptions","organizations_url":"https://api.github.com/users/PeteHaitch/orgs","repos_url":"https://api.github.com/users/PeteHaitch/repos","events_url":"https://api.github.com/users/PeteHaitch/events{/privacy}","received_events_url":"https://api.github.com/users/PeteHaitch/received_events","type":"User","site_admin":false},"labels":[{"id":947304434,"node_id":"MDU6TGFiZWw5NDczMDQ0MzQ=","url":"https://api.github.com/repos/COMBINE-lab/salmon/labels/alevin","name":"alevin","color":"e0d562","default":false},{"id":189596685,"node_id":"MDU6TGFiZWwxODk1OTY2ODU=","url":"https://api.github.com/repos/COMBINE-lab/salmon/labels/enhancement","name":"enhancement","color":"84b6eb","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-08-16T02:36:21Z","updated_at":"2018-08-27T18:37:16Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"I've just started working in a single-cell genomics core facility, **alevin** looks really useful for our 10X runs! \r\nBut I also have a substantial number of samples processed with the CEL-Seq and CEL-Seq2 protocols (also 3'-tag protocols). \r\nI'm interested in adding support for these protocols to Alevin.\r\n\r\n1. Is that something you'd be interested in incorporating?\r\n2. Any hints on where to start messing around in the code to implement this would be much appreciated!\r\n\r\nCheers,\r\nPete"},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/comments/416324900","html_url":"https://github.com/COMBINE-lab/salmon/issues/269#issuecomment-416324900","issue_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/269","id":416324900,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNjMyNDkwMA==","user":{"login":"k3yavi","id":8772521,"node_id":"MDQ6VXNlcjg3NzI1MjE=","avatar_url":"https://avatars3.githubusercontent.com/u/8772521?v=4","gravatar_id":"","url":"https://api.github.com/users/k3yavi","html_url":"https://github.com/k3yavi","followers_url":"https://api.github.com/users/k3yavi/followers","following_url":"https://api.github.com/users/k3yavi/following{/other_user}","gists_url":"https://api.github.com/users/k3yavi/gists{/gist_id}","starred_url":"https://api.github.com/users/k3yavi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/k3yavi/subscriptions","organizations_url":"https://api.github.com/users/k3yavi/orgs","repos_url":"https://api.github.com/users/k3yavi/repos","events_url":"https://api.github.com/users/k3yavi/events{/privacy}","received_events_url":"https://api.github.com/users/k3yavi/received_events","type":"User","site_admin":false},"created_at":"2018-08-27T18:37:16Z","updated_at":"2018-08-27T18:37:16Z","author_association":"COLLABORATOR","body":"Hey @PeteHaitch ,\r\nI think currently there is no direct way to tell Alevin to use CB and UMI in reverse order and you might have to hack a bit for that. Although it should not be too hard to do that. Specifically, the `extractBarcodes` and `extractUMI` function [here](https://github.com/COMBINE-lab/salmon/blob/master/src/AlevinUtils.cpp#L44) has to be updated with a new generic type (`celseq` may be). Let us know if it works out for you otherwise I can take a look into this sometime next week."}}
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