{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/76","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/76/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/76/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/76/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/76","id":79098529,"number":76,"title":"How to diagnose for lower coverage?","user":{"login":"yunfeiguo","id":7737294,"avatar_url":"https://avatars.githubusercontent.com/u/7737294?v=3","gravatar_id":"","url":"https://api.github.com/users/yunfeiguo","html_url":"https://github.com/yunfeiguo","followers_url":"https://api.github.com/users/yunfeiguo/followers","following_url":"https://api.github.com/users/yunfeiguo/following{/other_user}","gists_url":"https://api.github.com/users/yunfeiguo/gists{/gist_id}","starred_url":"https://api.github.com/users/yunfeiguo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yunfeiguo/subscriptions","organizations_url":"https://api.github.com/users/yunfeiguo/orgs","repos_url":"https://api.github.com/users/yunfeiguo/repos","events_url":"https://api.github.com/users/yunfeiguo/events{/privacy}","received_events_url":"https://api.github.com/users/yunfeiguo/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/labels/question","name":"question","color":"cc317c"},{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/labels/user_data","name":"user_data","color":"c7def8"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":16,"created_at":"2015-05-21T17:49:50Z","updated_at":"2015-05-22T20:47:37Z","closed_at":null,"body":"Dear Dr. Chin,\r\n\r\nWe have used a data set to do assembly and obtained 80% genome coverage, however, when more data comes in, we ran falcon from beginning and genome coverage dropped drastically to 2%.\r\n\r\nThe parameters are a little bit different, but I don't believe they are the main reason here. Could you give us some clues about what potentially are going wrong and how to find out? Thank you!\r\n\r\nParameters we used for 80% coverage:\r\n\r\n<pre>\r\n# The length cutoff used for seed reads used for initial mapping\r\nlength_cutoff = 6000\r\n\r\n# The length cutoff used for seed reads usef for pre-assembly\r\nlength_cutoff_pr = 6000\r\n\r\n#-M means limit memory usage, use integer\r\npa_HPCdaligner_option =  -v -dal128 -t16 -e.70 -l1000 -s1000\r\novlp_HPCdaligner_option = -v -dal128 -t32 -h60 -e.96 -l500 -s1000\r\n\r\n#-x is length threshold for including reads in DB\r\npa_DBsplit_option = -x500 -s400\r\novlp_DBsplit_option = -x500 -s400\r\n\r\nfalcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --local_match_count_threshold 2 --max_n_read 200 --n_core 8\r\n\r\noverlap_filtering_setting = --max_diff 60 --max_cov 60 --min_cov 2\r\n</pre>\r\n\r\nParameters we used for 2% coverage:\r\n\r\n<pre># The length cutoff used for seed reads used for initial mapping\r\nlength_cutoff = 6000\r\n\r\n# The length cutoff used for seed reads usef for pre-assembly\r\nlength_cutoff_pr = 6000\r\n\r\n#-M means limit memory usage, use integer\r\npa_HPCdaligner_option =  -v -dal128 -t16 -e.70 -l1000 -s1000\r\novlp_HPCdaligner_option = -v -dal128 -t32 -h60 -e.96 -l500 -s1000\r\n\r\n#-x is length threshold for including reads in DB\r\npa_DBsplit_option = -x500 -s400\r\novlp_DBsplit_option = -x500 -s400\r\n\r\nfalcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 6\r\n\r\noverlap_filtering_setting = --max_diff 40 --max_cov 25 --min_cov 2  --n_core 6\r\n</pre>"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/104763589","html_url":"https://github.com/PacificBiosciences/FALCON/issues/76#issuecomment-104763589","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/76","id":104763589,"user":{"login":"yunfeiguo","id":7737294,"avatar_url":"https://avatars.githubusercontent.com/u/7737294?v=3","gravatar_id":"","url":"https://api.github.com/users/yunfeiguo","html_url":"https://github.com/yunfeiguo","followers_url":"https://api.github.com/users/yunfeiguo/followers","following_url":"https://api.github.com/users/yunfeiguo/following{/other_user}","gists_url":"https://api.github.com/users/yunfeiguo/gists{/gist_id}","starred_url":"https://api.github.com/users/yunfeiguo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yunfeiguo/subscriptions","organizations_url":"https://api.github.com/users/yunfeiguo/orgs","repos_url":"https://api.github.com/users/yunfeiguo/repos","events_url":"https://api.github.com/users/yunfeiguo/events{/privacy}","received_events_url":"https://api.github.com/users/yunfeiguo/received_events","type":"User","site_admin":false},"created_at":"2015-05-22T20:47:37Z","updated_at":"2015-05-22T20:47:37Z","body":"Thanks for comments of overlap histograms. Very informative! If 30 is a good choice, then I guess I should be fine with 25 max coverage.\r\n\r\nFor preads4falcon.fasta, I found that this file is EXACTLY identical for different assemblies. For example, I have two preads4falcon.fasta generated in the following ways:\r\n1) in folder A, use subread filtered FASTA as input, specify `raw` in `fc_run.cfg`.\r\n2) create and enter another folder B, use `../A/1-preads_ovl/input_preads.fofn` as input, specify `preads` in `fc_run2.cfg`.\r\n`fc_run.cfg` and `fc_run2.cfg` differ by `--local_match_count_threshold`, ` --max_cov`,`--max_diff` options. \r\nWhat is going wrong here?"}}