{"action":"closed","issue":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/74","repository_url":"https://api.github.com/repos/gpertea/stringtie","labels_url":"https://api.github.com/repos/gpertea/stringtie/issues/74/labels{/name}","comments_url":"https://api.github.com/repos/gpertea/stringtie/issues/74/comments","events_url":"https://api.github.com/repos/gpertea/stringtie/issues/74/events","html_url":"https://github.com/gpertea/stringtie/issues/74","id":184692349,"number":74,"title":"StringTie's output TPM for downstream CuffDiff analysis","user":{"login":"boya888","id":8225801,"avatar_url":"https://avatars.githubusercontent.com/u/8225801?v=3","gravatar_id":"","url":"https://api.github.com/users/boya888","html_url":"https://github.com/boya888","followers_url":"https://api.github.com/users/boya888/followers","following_url":"https://api.github.com/users/boya888/following{/other_user}","gists_url":"https://api.github.com/users/boya888/gists{/gist_id}","starred_url":"https://api.github.com/users/boya888/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/boya888/subscriptions","organizations_url":"https://api.github.com/users/boya888/orgs","repos_url":"https://api.github.com/users/boya888/repos","events_url":"https://api.github.com/users/boya888/events{/privacy}","received_events_url":"https://api.github.com/users/boya888/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-10-23T14:11:35Z","updated_at":"2016-11-14T15:25:19Z","closed_at":"2016-11-14T15:25:19Z","body":"Thanks Pertea and collegues and for sharing the fascinating HISAT-StringTie-Ballgown pipeline, presented in NatureProtocol and NatureBiotech.\nNow we are reprocessing the RNA-seq data using your pipeline. However, we have encounter one bottleneck in using the output of StringTie for the following Differential Expression analysis, since we can't obtain enough replicates data (>=3, but we just can deposit 2 replicates data) from NCBI SRA. \nSo we try to use CuffDiff (support 2 replicates) to tackle this bottleneck.\n\nFortunately, we noted that you have mentioned that StringTie's output can be processed by specialized software like Cuffdiff in StringTie's homepage.\nHowever, we have no idea about Library normalization methods and \nhttp://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#cross-replicate-dispersion-estimation-methods \nCuffdiff can use a global model for all conditions.\n\nShould we use this when obtain the TPM from different samples and for further differential expression analysis?\nSo we post this mail for your suggestion on the parameter settings of CuffDiff to analyze the output of StringTie.\n"}}
{"actor":{"display_login":"gpertea"}}