Mercurial > repos > pjbriggs > pal_finder
comparison pal_finder_wrapper.xml @ 9:b3ca3ece8a8b draft
WIP detect/trap "bad primer product range" errors.
| author | pjbriggs |
|---|---|
| date | Fri, 16 Jun 2017 09:12:09 -0400 |
| parents | 67ab365c29a7 |
| children | 84613d5f1713 |
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| 8:67ab365c29a7 | 9:b3ca3ece8a8b |
|---|---|
| 272 primer3_core can be found in the Primer3 manual at | 272 primer3_core can be found in the Primer3 manual at |
| 273 http://primer3.sourceforge.net/primer3_manual.htm | 273 http://primer3.sourceforge.net/primer3_manual.htm |
| 274 | 274 |
| 275 ------------- | 275 ------------- |
| 276 | 276 |
| 277 .. class:: warning | |
| 278 | |
| 279 **Known problems** | |
| 280 | |
| 281 .. class:: infomark | |
| 282 | |
| 283 **Bad primer product size ranges** | |
| 284 | |
| 285 For some datasets pal_finder may generate 'bad' product size ranges (where the | |
| 286 lower limit exceeds the upper limit) for one or more reads, for input into | |
| 287 primer3_core. | |
| 288 | |
| 289 If this occurs then the tool will terminate with an error. A list of the reads | |
| 290 for which the bad ranges were generated can be found in the error message | |
| 291 which can be accessed via the 'bug' icon from a failed dataset. | |
| 292 | |
| 293 The conditions which cause this error are unclear. However we believe it to be | |
| 294 associated with short or low quality reads. It is recommended that the input | |
| 295 data are sufficiently trimmed and filtered (using e.g. the Trimmomatic tool) | |
| 296 before rerunning pal_finder. | |
| 297 | |
| 298 ------------- | |
| 299 | |
| 277 .. class:: infomark | 300 .. class:: infomark |
| 278 | 301 |
| 279 **Credits** | 302 **Credits** |
| 280 | 303 |
| 281 This Galaxy tool has been developed by Peter Briggs within the Bioinformatics Core | 304 This Galaxy tool has been developed by Peter Briggs within the Bioinformatics Core |