{"action":"created","issue":{"url":"https://api.github.com/repos/zd1/telseq/issues/9","repository_url":"https://api.github.com/repos/zd1/telseq","labels_url":"https://api.github.com/repos/zd1/telseq/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/zd1/telseq/issues/9/comments","events_url":"https://api.github.com/repos/zd1/telseq/issues/9/events","html_url":"https://github.com/zd1/telseq/issues/9","id":162726995,"number":9,"title":"UNKNOWN length estimate using exome sequencing data","user":{"login":"ikramu","id":1573674,"avatar_url":"https://avatars.githubusercontent.com/u/1573674?v=3","gravatar_id":"","url":"https://api.github.com/users/ikramu","html_url":"https://github.com/ikramu","followers_url":"https://api.github.com/users/ikramu/followers","following_url":"https://api.github.com/users/ikramu/following{/other_user}","gists_url":"https://api.github.com/users/ikramu/gists{/gist_id}","starred_url":"https://api.github.com/users/ikramu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ikramu/subscriptions","organizations_url":"https://api.github.com/users/ikramu/orgs","repos_url":"https://api.github.com/users/ikramu/repos","events_url":"https://api.github.com/users/ikramu/events{/privacy}","received_events_url":"https://api.github.com/users/ikramu/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-06-28T16:17:19Z","updated_at":"2016-06-29T08:27:50Z","closed_at":null,"body":"Hi,\r\n\r\nI am using telseq on exome sequencing data using the following command\r\n\r\ntelseq -e ~/Downloads/telseq/targets.bed -f ~/Downloads/telseq/fileList.txt ~/Downloads/telseq/telseqOutput.txt\r\nIn the output, although I get estimates for the number of reads at different \"k\" and GC-adjusted coverage, I am getting UNKNOWN for the length estimate. \r\n\r\nHere is one line from my output\r\nReadGroup       Library Sample  Total   Mapped  Duplicates      LENGTH_ESTIMATE TEL0    TEL1    TEL2    TEL3    TEL4    TEL5    TEL6    TEL7    TEL8    TEL9    TEL10   TEL11   TEL12   TEL13   TEL14   TEL15   TEL16   GC0     GC1     GC2     GC3     GC4     GC5     GC6     GC7     GC8     GC9     \r\n0       UNKNOWN Patient10        10743572        10743501        3112566 UNKNOWN 10499798        241583  2140    51      0       0       0       0       0       0       0       0       0\r\n       0       0       0       0       579891  1001440 944504  785288  703376  364539  587419  618909  608799  558685  \r\n\r\nCan someone assist me as to where I may be wrong?\r\n\r\nCheers,\r\nIkram"},"comment":{"url":"https://api.github.com/repos/zd1/telseq/issues/comments/229290565","html_url":"https://github.com/zd1/telseq/issues/9#issuecomment-229290565","issue_url":"https://api.github.com/repos/zd1/telseq/issues/9","id":229290565,"user":{"login":"zd1","id":814295,"avatar_url":"https://avatars.githubusercontent.com/u/814295?v=3","gravatar_id":"","url":"https://api.github.com/users/zd1","html_url":"https://github.com/zd1","followers_url":"https://api.github.com/users/zd1/followers","following_url":"https://api.github.com/users/zd1/following{/other_user}","gists_url":"https://api.github.com/users/zd1/gists{/gist_id}","starred_url":"https://api.github.com/users/zd1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zd1/subscriptions","organizations_url":"https://api.github.com/users/zd1/orgs","repos_url":"https://api.github.com/users/zd1/repos","events_url":"https://api.github.com/users/zd1/events{/privacy}","received_events_url":"https://api.github.com/users/zd1/received_events","type":"User","site_admin":false},"created_at":"2016-06-29T08:27:50Z","updated_at":"2016-06-29T08:27:50Z","body":"Hi Ikram,\n\nThanks for your interests in using telseq. It seems that there's no reads\nbeyond TEL4, meaning reads containing four telomeric repeats. Have you\ntried running it without \"-e\" ?\n\nCheers,\nZhihao\n\n\n\nOn 28 June 2016 at 17:17, Ikram Ullah <notifications@github.com> wrote:\n\n> Hi,\n>\n> I am using telseq on exome sequencing data using the following command\n>\n> telseq -e ~/Downloads/telseq/targets.bed -f\n> ~/Downloads/telseq/fileList.txt ~/Downloads/telseq/telseqOutput.txt\n> In the output, although I get estimates for the number of reads at\n> different \"k\" and GC-adjusted coverage, I am getting UNKNOWN for the length\n> estimate.\n>\n> Here is one line from my output\n> ReadGroup Library Sample Total Mapped Duplicates LENGTH_ESTIMATE TEL0 TEL1\n> TEL2 TEL3 TEL4 TEL5 TEL6 TEL7 TEL8 TEL9 TEL10 TEL11 TEL12 TEL13 TEL14 TEL15\n> TEL16 GC0 GC1 GC2 GC3 GC4 GC5 GC6 GC7 GC8 GC9\n>\n> 0 UNKNOWN Patient10 10743572 10743501 3112566 UNKNOWN 10499798 241583 2140\n> 51 0 0 0 0 0 0 0 0 0\n> 0 0 0 0 579891 1001440 944504 785288 703376 364539 587419 618909 608799\n> 558685\n>\n> Can someone assist me as to where I may be wrong?\n>\n> Cheers,\n> Ikram\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/zd1/telseq/issues/9>, or mute the thread\n> <https://github.com/notifications/unsubscribe/AAxs15cVZ-09BgFJwht3sKk4dfNY6Kseks5qQUkPgaJpZM4JARvb>\n> .\n>\n\n-- \nThis email is sent on behalf of Genomics plc, a public limited company \nregistered in England and Wales with registered number 8839972, VAT \nregistered number 189 2635 65 and registered office at 24 Cornhill, London, \nEC3V 3ND, United Kingdom.\nThe contents of this e-mail and any attachments are confidential to the \nintended recipient. 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