{"action":"closed","issue":{"url":"https://api.github.com/repos/benjjneb/dada2/issues/44","labels_url":"https://api.github.com/repos/benjjneb/dada2/issues/44/labels{/name}","comments_url":"https://api.github.com/repos/benjjneb/dada2/issues/44/comments","events_url":"https://api.github.com/repos/benjjneb/dada2/issues/44/events","html_url":"https://github.com/benjjneb/dada2/issues/44","id":109719961,"number":44,"title":"Length variation in the dada2 output","user":{"login":"jeffkimbrel","id":10132972,"avatar_url":"https://avatars.githubusercontent.com/u/10132972?v=3","gravatar_id":"","url":"https://api.github.com/users/jeffkimbrel","html_url":"https://github.com/jeffkimbrel","followers_url":"https://api.github.com/users/jeffkimbrel/followers","following_url":"https://api.github.com/users/jeffkimbrel/following{/other_user}","gists_url":"https://api.github.com/users/jeffkimbrel/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffkimbrel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffkimbrel/subscriptions","organizations_url":"https://api.github.com/users/jeffkimbrel/orgs","repos_url":"https://api.github.com/users/jeffkimbrel/repos","events_url":"https://api.github.com/users/jeffkimbrel/events{/privacy}","received_events_url":"https://api.github.com/users/jeffkimbrel/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-10-05T02:07:54Z","updated_at":"2015-10-14T17:48:16Z","closed_at":"2015-10-14T17:48:16Z","body":"First off, dada2 is great... I love software that just works with easy installation, and with a clear pipeline as outlined in the tutorial.\r\n\r\nSecond, sorry if this is the wrong place for this, since it isn't necessarily a software issue, but I have a question about results interpretation.\r\n\r\nIn the tutorial, there was a very tight spread in the lengths of sequences returned, and it mentions...\r\n\r\n>large length differences in the 16S region, especially after merging, are typically caused by alternate priming from non-specific primers. If this is not controlled for, this can produce false variation in the output.\r\n\r\nBelow is my output, and there is a very large variation in length, although most of the sequences are between 230-235nt.\r\n\r\n```\r\ntable(nchar(colnames(seqtab)))\r\n## \r\n## 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 \r\n## 329   9  10 386  12  12   7   5   9   7   4   3  10   6  11   8  16   7 \r\n## 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 \r\n##   9   2   8   4  10  11   9   4   6   9  11   7   8   6   4   9   6   7 \r\n## 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 \r\n##  14   6   7  10   5   7   7   9   7  16   9   7   8   8  12   8   7   5 \r\n## 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 \r\n##   9  13   7   9  10   6  12  10  11   7   7  11  12   8   7  16  12  11 \r\n## 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 \r\n##  13   8  11   9   8  14  10  12  10  11  11  17  13  14  12  12  11  11 \r\n## 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 \r\n##   7  21  21  13  20  28  17  16  15  18  12  12  18  13  18  12  14  11 \r\n## 338 339 340 341 342 343 344 345 346 347 348 349 \r\n##  14  16  18  15  13  22  10  12  16  15  19  19\r\n```\r\n\r\nI am wondering how do you recommend controlling or correcting for this potential variation? Should I just ignore all sequences greater than ~235? My quality assessments were similar to those in the tutorial, and I trimmed to 10-240 for the forward, and 10-150 for the reverse sequences.\r\n\r\nThanks,\r\n\r\nJeff"}}