{"action":"created","issue":{"url":"https://api.github.com/repos/aboyle/F-seq/issues/8","repository_url":"https://api.github.com/repos/aboyle/F-seq","labels_url":"https://api.github.com/repos/aboyle/F-seq/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/aboyle/F-seq/issues/8/comments","events_url":"https://api.github.com/repos/aboyle/F-seq/issues/8/events","html_url":"https://github.com/aboyle/F-seq/issues/8","id":25310257,"number":8,"title":"F-seq 1.85 results are quite different to 1.84 results","user":{"login":"ghuls","id":1299177,"avatar_url":"https://avatars.githubusercontent.com/u/1299177?v=3","gravatar_id":"","url":"https://api.github.com/users/ghuls","html_url":"https://github.com/ghuls","followers_url":"https://api.github.com/users/ghuls/followers","following_url":"https://api.github.com/users/ghuls/following{/other_user}","gists_url":"https://api.github.com/users/ghuls/gists{/gist_id}","starred_url":"https://api.github.com/users/ghuls/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ghuls/subscriptions","organizations_url":"https://api.github.com/users/ghuls/orgs","repos_url":"https://api.github.com/users/ghuls/repos","events_url":"https://api.github.com/users/ghuls/events{/privacy}","received_events_url":"https://api.github.com/users/ghuls/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2014-01-09T10:58:52Z","updated_at":"2016-03-31T14:51:43Z","closed_at":"2016-03-31T14:51:43Z","body":"When running F-seq 1.84 and 1.85 on the same BED file and outputting in BED format, I get quite different results:\r\n\r\n```bash\r\n$ /software/fseq/fseq-1.84/bin/fseq -of bed -o fseq-1.84 test_chr21_22_Y.bed\r\n\r\n$ /software/fseq/fseq-1.85/bin/fseq -of bed -o fseq-1.85 test_chr21_22_Y.bed\r\n```\r\n\r\nF-seq 1.84 and F-seq 1.85 results have quite a different number of regions:\r\n\r\n``` bash\r\n$ wc -l fseq-1.84/*.bed\r\n   3639 fseq-1.84/chr21.bed\r\n  35229 fseq-1.84/chr22.bed\r\n    659 fseq-1.84/chrY.bed\r\n  39527 total\r\n\r\n$ wc -l fseq-1.85/*.bed\r\n   4198 fseq-1.85/chr21.bed\r\n  34741 fseq-1.85/chr22.bed\r\n    545 fseq-1.85/chrY.bed\r\n  39484 total\r\n```\r\n\r\n``` bash\r\n$ head fseq-1.84/chr21.bed fseq-1.85/chr21.bed\r\n==> fseq-1.84/chr21.bed <==\r\nchr21\t9411332\t9411337\tchr21.1\t0.48834208\r\nchr21\t9415188\t9415349\tchr21.2\t0.6090521\r\nchr21\t9416306\t9416373\tchr21.3\t0.49469206\r\nchr21\t9417096\t9417173\tchr21.4\t0.65191275\r\nchr21\t9418952\t9419068\tchr21.5\t0.6870976\r\nchr21\t9423002\t9423017\tchr21.6\t0.49764535\r\nchr21\t9423021\t9423056\tchr21.7\t0.4918731\r\nchr21\t9425367\t9425391\tchr21.8\t0.541325\r\nchr21\t9425414\t9425438\tchr21.9\t0.4980668\r\nchr21\t9425741\t9425783\tchr21.10\t0.5575222\r\n\r\n==> fseq-1.85/chr21.bed <==\r\nchr21\t9411332\t9411337\tchr21.1\t0.5120084\r\nchr21\t9411339\t9411367\tchr21.2\t0.461942\r\nchr21\t9415167\t9415357\tchr21.3\t0.68790144\r\nchr21\t9416264\t9416373\tchr21.4\t0.5575416\r\nchr21\t9417096\t9417174\tchr21.5\t0.6494265\r\nchr21\t9417680\t9417694\tchr21.6\t0.4830733\r\nchr21\t9418938\t9419128\tchr21.7\t0.73948044\r\nchr21\t9420954\t9420998\tchr21.8\t0.49452877\r\nchr21\t9421034\t9421078\tchr21.9\t0.48758772\r\nchr21\t9421095\t9421103\tchr21.10\t0.4895442\r\n```\r\n\r\n\r\nWhen running F-seq 1.84 and 1.85 on the same BED file and outputting in wig format, I get quite different results:\r\n\r\n```bash\r\n$ /software/fseq/fseq-1.84/bin/fseq -of wig -o fseq-1.84 test_chr21_22_Y.bed\r\n\r\n$ /software/fseq/fseq-1.85/bin/fseq -of wig -o fseq-1.85 test_chr21_22_Y.bed\r\n```\r\n\r\n``` bash\r\n$ head fseq-1.84/chr21.wig fseq-1.85/chr21.wig\r\n==> fseq-1.84/chr21.wig <==\r\nfixedStep chrom=chr21 start=9411238 step=1\r\n0.2358\r\n0.2371\r\n0.3032\r\n0.3047\r\n0.3061\r\n0.3075\r\n0.3089\r\n0.3102\r\n0.3116\r\n\r\n==> fseq-1.85/chr21.wig <==\r\nfixedStep chrom=chr21 start=9411238 step=1\r\n0.2649\r\n0.2661\r\n0.3218\r\n0.3233\r\n0.3248\r\n0.3263\r\n0.3278\r\n0.3292\r\n0.3306\r\n```\r\n\r\nWhy are the results so different between the versions, and which one gives the most correct result?"},"comment":{"url":"https://api.github.com/repos/aboyle/F-seq/issues/comments/203973201","html_url":"https://github.com/aboyle/F-seq/issues/8#issuecomment-203973201","issue_url":"https://api.github.com/repos/aboyle/F-seq/issues/8","id":203973201,"user":{"login":"aboyle","id":847955,"avatar_url":"https://avatars.githubusercontent.com/u/847955?v=3","gravatar_id":"","url":"https://api.github.com/users/aboyle","html_url":"https://github.com/aboyle","followers_url":"https://api.github.com/users/aboyle/followers","following_url":"https://api.github.com/users/aboyle/following{/other_user}","gists_url":"https://api.github.com/users/aboyle/gists{/gist_id}","starred_url":"https://api.github.com/users/aboyle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aboyle/subscriptions","organizations_url":"https://api.github.com/users/aboyle/orgs","repos_url":"https://api.github.com/users/aboyle/repos","events_url":"https://api.github.com/users/aboyle/events{/privacy}","received_events_url":"https://api.github.com/users/aboyle/received_events","type":"User","site_admin":false},"created_at":"2016-03-31T14:51:43Z","updated_at":"2016-03-31T14:51:43Z","body":"There is a bit of randomness in the threshold estimation of F-seq as well as the fragment size estimation because of the sub-sampling. Setting the threshold will make the behavior of the program consistent. "}}