{"action":"created","issue":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/292","repository_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq","labels_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/292/labels{/name}","comments_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/292/comments","events_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/292/events","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/292","id":238406711,"number":292,"title":"FPKM values from SE vs. PE RNA-Seq libraries","user":{"login":"santiagoha","id":16104926,"avatar_url":"https://avatars3.githubusercontent.com/u/16104926?v=3","gravatar_id":"","url":"https://api.github.com/users/santiagoha","html_url":"https://github.com/santiagoha","followers_url":"https://api.github.com/users/santiagoha/followers","following_url":"https://api.github.com/users/santiagoha/following{/other_user}","gists_url":"https://api.github.com/users/santiagoha/gists{/gist_id}","starred_url":"https://api.github.com/users/santiagoha/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/santiagoha/subscriptions","organizations_url":"https://api.github.com/users/santiagoha/orgs","repos_url":"https://api.github.com/users/santiagoha/repos","events_url":"https://api.github.com/users/santiagoha/events{/privacy}","received_events_url":"https://api.github.com/users/santiagoha/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-06-25T21:10:11Z","updated_at":"2017-06-26T11:28:00Z","closed_at":null,"body":"I have a question regarding the use of RSEM for estimating isoform expression levels. I have 5 different RNA-Seq assemblies (4 are single-end and the remaining one is paired-end) from different species of the same tissue. The species are divided in two groups (A and B) and I'm interested in looking at the expression profiles of some genes between the two groups. When I use Trinity's Transcript Quantification protocol with RSEM, I get very different FPKM values for the SE assemblies compared to the PE assembly. For one gene I'm getting the following values (and it is very similar with the other genes):\r\n\r\nSE assemblies: 424 (group A), 381.8 (group A), 471 (group A), 115.3 (group B)\r\n\r\nPE assemblies: 1.74 (group B)\r\n\r\nAs you can see, there's a difference of two orders of magnitude between assemblies, and this difference occurs within the same species group (B). So, does the FPKM values from SE and PE libraries can be directly compared? Is there a way to do a correction for the different amount of reads between SE and PE libraries?\r\n\r\nAny suggestion is very welcome, thanks!!\r\n\r\nPS. The same situation occurs with TPM values"},"comment":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/comments/311033173","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/292#issuecomment-311033173","issue_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/292","id":311033173,"user":{"login":"brianjohnhaas","id":7542111,"avatar_url":"https://avatars3.githubusercontent.com/u/7542111?v=3","gravatar_id":"","url":"https://api.github.com/users/brianjohnhaas","html_url":"https://github.com/brianjohnhaas","followers_url":"https://api.github.com/users/brianjohnhaas/followers","following_url":"https://api.github.com/users/brianjohnhaas/following{/other_user}","gists_url":"https://api.github.com/users/brianjohnhaas/gists{/gist_id}","starred_url":"https://api.github.com/users/brianjohnhaas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brianjohnhaas/subscriptions","organizations_url":"https://api.github.com/users/brianjohnhaas/orgs","repos_url":"https://api.github.com/users/brianjohnhaas/repos","events_url":"https://api.github.com/users/brianjohnhaas/events{/privacy}","received_events_url":"https://api.github.com/users/brianjohnhaas/received_events","type":"User","site_admin":false},"created_at":"2017-06-26T11:28:00Z","updated_at":"2017-06-26T11:28:00Z","body":"Hi\n\nJust for curiosity can you try running the PE quant as if it were SE and see how that compares?\n\nI'd suggest looking at pairwise correlations for a number of transcripts to see if there's z systematic difference.  Also try comparing TPM vals instead of fpkm \n\nBest\n\n-Brian\n(by iPhone)\n\n\n> On Jun 25, 2017, at 5:10 PM, santiagoha <notifications@github.com> wrote:\n> \n> I have a question regarding the use of RSEM for estimating isoform expression levels. I have 5 different RNA-Seq assemblies (4 are single-end and the remaining one is paired-end) from different species of the same tissue. The species are divided in two groups (A and B) and I'm interested in looking at the expression profiles of some genes between the two groups. When I use Trinity's Transcript Quantification protocol with RSEM, I get very different FPKM values for the SE assemblies compared to the PE assembly. For one gene I'm getting the following values (and it is very similar with the other genes):\n> \n> SE assemblies: 424 (group A), 381.8 (group A), 471 (group A), 115.3 (group B)\n> \n> PE assemblies: 1.74 (group B)\n> \n> As you can see, there's a difference of two orders of magnitude between assemblies, and this difference occurs within the same species group (B). So, does the FPKM values from SE and PE libraries can be directly compared? Is there a way to do a correction for the different amount of reads between SE and PE libraries?\n> \n> Any suggestion is very welcome, thanks!!\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub, or mute the thread.\n> \n"}}
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