{"action":"created","issue":{"url":"https://api.github.com/repos/mhammell-laboratory/tetoolkit/issues/5","repository_url":"https://api.github.com/repos/mhammell-laboratory/tetoolkit","labels_url":"https://api.github.com/repos/mhammell-laboratory/tetoolkit/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/mhammell-laboratory/tetoolkit/issues/5/comments","events_url":"https://api.github.com/repos/mhammell-laboratory/tetoolkit/issues/5/events","html_url":"https://github.com/mhammell-laboratory/tetoolkit/pull/5","id":156092801,"number":5,"title":"TEcount","user":{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars.githubusercontent.com/u/6399000?v=3","gravatar_id":"","url":"https://api.github.com/users/dpryan79","html_url":"https://github.com/dpryan79","followers_url":"https://api.github.com/users/dpryan79/followers","following_url":"https://api.github.com/users/dpryan79/following{/other_user}","gists_url":"https://api.github.com/users/dpryan79/gists{/gist_id}","starred_url":"https://api.github.com/users/dpryan79/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpryan79/subscriptions","organizations_url":"https://api.github.com/users/dpryan79/orgs","repos_url":"https://api.github.com/users/dpryan79/repos","events_url":"https://api.github.com/users/dpryan79/events{/privacy}","received_events_url":"https://api.github.com/users/dpryan79/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"status-five","id":9337053,"avatar_url":"https://avatars.githubusercontent.com/u/9337053?v=3","gravatar_id":"","url":"https://api.github.com/users/status-five","html_url":"https://github.com/status-five","followers_url":"https://api.github.com/users/status-five/followers","following_url":"https://api.github.com/users/status-five/following{/other_user}","gists_url":"https://api.github.com/users/status-five/gists{/gist_id}","starred_url":"https://api.github.com/users/status-five/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/status-five/subscriptions","organizations_url":"https://api.github.com/users/status-five/orgs","repos_url":"https://api.github.com/users/status-five/repos","events_url":"https://api.github.com/users/status-five/events{/privacy}","received_events_url":"https://api.github.com/users/status-five/received_events","type":"User","site_admin":false},"milestone":null,"comments":3,"created_at":"2016-05-21T09:22:50Z","updated_at":"2016-05-24T17:56:01Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/mhammell-laboratory/tetoolkit/pulls/5","html_url":"https://github.com/mhammell-laboratory/tetoolkit/pull/5","diff_url":"https://github.com/mhammell-laboratory/tetoolkit/pull/5.diff","patch_url":"https://github.com/mhammell-laboratory/tetoolkit/pull/5.patch"},"body":"This PR adds `TEcount`, a modified version of TEtranscripts that only generates count tables and doesn't require multiple samples. This is a huge time saver, since this can then be run in parallel on each sample.\r\n\r\nAnother difference with `TEcount`, that you may or may not find useful, is that it presplits the counts into multiple files. So you get one file of gene counts, another of TE families, and so on. These can be used in DESeq2 conveniently with `DESeqDatasetFromHTSeqCount()`."},"comment":{"url":"https://api.github.com/repos/mhammell-laboratory/tetoolkit/issues/comments/221352387","html_url":"https://github.com/mhammell-laboratory/tetoolkit/pull/5#issuecomment-221352387","issue_url":"https://api.github.com/repos/mhammell-laboratory/tetoolkit/issues/5","id":221352387,"user":{"login":"status-five","id":9337053,"avatar_url":"https://avatars.githubusercontent.com/u/9337053?v=3","gravatar_id":"","url":"https://api.github.com/users/status-five","html_url":"https://github.com/status-five","followers_url":"https://api.github.com/users/status-five/followers","following_url":"https://api.github.com/users/status-five/following{/other_user}","gists_url":"https://api.github.com/users/status-five/gists{/gist_id}","starred_url":"https://api.github.com/users/status-five/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/status-five/subscriptions","organizations_url":"https://api.github.com/users/status-five/orgs","repos_url":"https://api.github.com/users/status-five/repos","events_url":"https://api.github.com/users/status-five/events{/privacy}","received_events_url":"https://api.github.com/users/status-five/received_events","type":"User","site_admin":false},"created_at":"2016-05-24T17:56:01Z","updated_at":"2016-05-24T17:56:01Z","body":"**Test Results:**\r\n\r\n```\r\n13:45:13 dmolik@maritimus.cshl {~/tetoolkit}$ TEcount -b ~/Downloads/test_data_SE_control.bam --GTF ~/Downloads/dm3_refGene.gtf --TE ~/Downloads/dm3_rmsk_TE.gtf\r\nINFO  @ Tue, 24 May 2016 13:45:34: \r\n# ARGUMENTS LIST:\r\n# name = TEtranscripts_out\r\n# treatment files = /Users/dmolik/Downloads/test_data_SE_control.bam\r\n# control files = \r\n# GTF file = /Users/dmolik/Downloads/dm3_refGene.gtf \r\n# TE file = /Users/dmolik/Downloads/dm3_rmsk_TE.gtf \r\n# multi-mapper mode = multi \r\n# stranded = yes \r\n# normalization = NA (rpm: Reads Per Million mapped; quant: Quantile normalization)\r\n# FDR cutoff = 1.00e+00\r\n# fold-change cutoff =  0.00\r\n# read count cutoff = 0\r\n# number of iteration = 100\r\n# Alignments grouped by read ID = True\r\n\r\n \r\nINFO  @ Tue, 24 May 2016 13:45:34: Processing GTF files ...\r\n \r\nINFO  @ Tue, 24 May 2016 13:45:34: Building gene index .......\r\n \r\n100000 GTF lines processed.\r\nINFO  @ Tue, 24 May 2016 13:45:52: Done building gene index ......\r\n \r\nINFO  @ Tue, 24 May 2016 13:45:53: \r\nBuilding TE index .......\r\n \r\nINFO  @ Tue, 24 May 2016 13:46:02: Done building TE index ......\r\n \r\nINFO  @ Tue, 24 May 2016 13:46:02: \r\nReading sample file ...\r\n \r\n1000000 alignments  processed.\r\nuniq te counts = 487199.0 \r\n.......start iterative optimization ..........\r\nmulti-reads = 364 total means = 1.33146462749\r\nafter normalization toatl means0 = 1.0\r\nSQUAREM iteraton [1]\r\n1/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.67217302262\r\nafter normalization toatl means = 1.0\r\n2/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.82868343589\r\nafter normalization toatl means = 1.0\r\nalpha = 1.0, SQUAREM iteraton [2]\r\n1/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.90789144035\r\nafter normalization toatl means = 1.0\r\n2/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.94688592856\r\nafter normalization toatl means = 1.0\r\nalpha = 1.45717813976.\r\n Performing a stabilization step.\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.97948495991\r\nafter normalization toatl means = 1.0\r\nalpha = 1.45717813976, SQUAREM iteraton [3]\r\n1/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.98253528257\r\nafter normalization toatl means = 1.0\r\n2/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.98422404596\r\nafter normalization toatl means = 1.0\r\nalpha = 1.42019425179.\r\n Performing a stabilization step.\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.98587656212\r\nafter normalization toatl means = 1.0\r\nalpha = 1.42019425179, SQUAREM iteraton [4]\r\n1/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.98618675712\r\nafter normalization toatl means = 1.0\r\n2/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.98640178912\r\nafter normalization toatl means = 1.0\r\nalpha = 2.13636845923.\r\n Performing a stabilization step.\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.98684179272\r\nafter normalization toatl means = 1.0\r\nalpha = 2.13636845923, SQUAREM iteraton [5]\r\n1/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.98690797474\r\nafter normalization toatl means = 1.0\r\n2/3\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\ntotal multi counts = 361.0\r\ntotal means = 1.98696791851\r\nafter normalization toatl means = 1.0\r\nrNome = OPT_TOL \r\nconverge at iteration 5\r\nnum of multi reads = 364\r\ntotal multi counts = 361.0\r\nTE counts total 487560.0\r\nGene counts total 212935.571825\r\n\r\nIn library /Users/dmolik/Downloads/test_data_SE_control.bam:\r\nTotal annotated reads = 700495.571825\r\nTotal non-uniquely mapped reads = 1970\r\nTotal unannotated reads = 741078\r\n\r\nINFO  @ Tue, 24 May 2016 13:46:39: Finished processing sample file\r\n```"}}
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