| f6d2005 | spleonard1 | 06 December 2016, 18:09:12 UTC | script to count TA sites not general | 06 December 2016, 18:09:12 UTC |
| 62964b5 | spleonard1 | 06 December 2016, 17:51:16 UTC | Test new folder | 06 December 2016, 17:51:16 UTC |
| 9e368f9 | spleonard1 | 06 December 2016, 17:48:51 UTC | Updated Essential Script to use a list of TA sites | 06 December 2016, 17:48:51 UTC |
| 1a53163 | Sean Leonard | 02 May 2016, 22:31:58 UTC | Fixed counting in TnSeq2.sh with new illumina headers | 02 May 2016, 22:31:58 UTC |
| 0c0ab99 | Sean Leonard | 16 February 2016, 17:28:08 UTC | Changed default site filtering behavior | 16 February 2016, 17:28:08 UTC |
| c5da1de | Sean Leonard | 16 February 2016, 17:26:58 UTC | Changed instructions in Essential Script | 16 February 2016, 17:26:58 UTC |
| 7166acd | Sean Leonard | 26 January 2016, 19:33:39 UTC | Add ^@K to count all reads | 26 January 2016, 19:33:39 UTC |
| 1d22c91 | Sean Leonard | 26 January 2016, 01:43:48 UTC | Fixed skipping header lines | 26 January 2016, 01:43:48 UTC |
| 6d219e8 | Sean Leonard | 12 January 2016, 06:34:31 UTC | no KO or Pathway in analysis. Removed normalization by site prior to DE analysis | 12 January 2016, 06:34:31 UTC |
| 9fb4163 | Sean Leonard | 11 January 2016, 06:48:33 UTC | Removed normalization by site | 11 January 2016, 06:48:33 UTC |
| ca711bb | Sean Leonard | 11 January 2016, 06:43:06 UTC | Removed requirement for KEGG or Pathway in gff file | 11 January 2016, 06:43:06 UTC |
| a09663f | Sean Leonard | 08 January 2016, 20:41:02 UTC | Fixed results output. No more KEGG or Pathways | 08 January 2016, 20:41:02 UTC |
| 807938f | Sean Leonard | 08 January 2016, 02:34:09 UTC | Fixed permissions and added .gitignore | 08 January 2016, 02:34:09 UTC |
| 6f5c196 | Sean Leonard | 08 January 2016, 02:16:40 UTC | Fix permissions | 08 January 2016, 02:16:40 UTC |
| d3e02bb | Sean Leonard | 08 January 2016, 01:30:47 UTC | Fixed to use 'flexbar_execuable' | 08 January 2016, 01:30:47 UTC |
| 119aa64 | Sean Leonard | 06 January 2016, 23:16:57 UTC | Fix PullKegg to work with website changes | 06 January 2016, 23:16:57 UTC |
| ad138f2 | Sean Leonard | 06 January 2016, 22:30:54 UTC | Some cleanup for manuscript prep | 06 January 2016, 22:30:54 UTC |
| febb2e5 | Sean Leonard | 15 June 2015, 17:56:28 UTC | removed DESeq call, just using manual normalization factor of 1 | 15 June 2015, 17:56:28 UTC |
| 730c76f | Sean Leonard | 12 June 2015, 18:33:24 UTC | Removed expired scripts | 12 June 2015, 18:33:24 UTC |
| 34fab51 | Sean Leonard | 12 June 2015, 17:58:23 UTC | Added site filtering for TnSeqDESeq2.R | 12 June 2015, 17:58:23 UTC |
| 571281a | Sean Leonard | 12 June 2015, 05:04:48 UTC | Essential and differential scripts working with DESeq2 | 12 June 2015, 05:04:48 UTC |
| 8f4e3d9 | Sean Leonard | 11 June 2015, 20:34:49 UTC | Call new DESeq2 R script | 11 June 2015, 20:34:49 UTC |
| 1cb676e | Sean Leonard | 11 June 2015, 20:31:01 UTC | Update assembly prefix for genomes | 11 June 2015, 20:31:01 UTC |
| 2ff9d59 | Sean Leonard | 10 June 2015, 01:01:01 UTC | Added site filtering, corrected genome length increase by 10% | 10 June 2015, 01:01:01 UTC |
| 483a2b7 | Sean Leonard | 09 June 2015, 18:13:38 UTC | include site filtering(2 sites by default) | 09 June 2015, 18:13:38 UTC |
| 9343af4 | Sean Leonard | 09 June 2015, 06:08:57 UTC | Essentials Script updated to use DESeq2. No change? | 09 June 2015, 06:08:57 UTC |
| ea0847a | Sean Leonard | 22 May 2015, 03:27:17 UTC | Fix PullKegg.pl and remved tbl_df calls | 22 May 2015, 03:27:17 UTC |
| 5c2da35 | Sean Leonard | 22 May 2015, 03:25:34 UTC | Removed tbl_df calls | 22 May 2015, 03:25:34 UTC |
| 0797e7d | Sean Leonard | 20 May 2015, 20:36:12 UTC | Update to include TnSeqDESeq2.R | 20 May 2015, 20:36:12 UTC |
| 8f168a7 | Sean Leonard | 07 April 2015, 20:16:24 UTC | Update DESeq with DESeq2 | 07 April 2015, 20:16:24 UTC |
| 50e5490 | Keith H. Turner | 12 November 2014, 21:56:06 UTC | Update README.md | 12 November 2014, 21:56:06 UTC |
| b0df854 | Keith H. Turner | 23 October 2014, 19:22:03 UTC | Error in the handling of duplicate reads Previously, reads were filtered on MAPQ. However, MAPQ heavily penalizes reads for not mapping uniquely, which occurs often in repeated regions of bacterial genomes. To correct this, post-adapter trimming length was increased to 35 to increase the ability to accurately uniquely map trimmed reads, and bowtie2 was put into "-a" mode, which reports all matches. As these are reported in descending order of alignment score, with ties randomly ordered, we can simply choose the first reported match for any single read to randomly assign ambiguous reads to one of its possible origins. Thus, transposon insertions that would yield identical reads from more than one location are impossible to place correctly in the genome and should be viewed with suspicion. | 23 October 2014, 19:22:03 UTC |
| 528b575 | Keith H. Turner | 23 October 2014, 19:20:33 UTC | Error in the handling of duplicate reads Previously, reads were filtered on MAPQ. However, MAPQ heavily penalizes reads for not mapping uniquely, which occurs often in repeated regions of bacterial genomes. To correct this, post-adapter trimming length was increased to 35 to increase the ability to accurately uniquely map trimmed reads, and bowtie2 was put into "-a" mode, which reports all matches. As these are reported in descending order of alignment score, with ties randomly ordered, we can simply choose the first reported match for any single read to randomly assign ambiguous reads to one of its possible origins. Thus, transposon insertions that would yield identical reads from more than one location are impossible to place correctly in the genome and should be viewed with suspicion. | 23 October 2014, 19:20:33 UTC |
| 0c3a1e6 | Keith H. Turner | 13 October 2014, 20:10:30 UTC | Update TnSeq.sh | 13 October 2014, 20:10:30 UTC |
| 3c63dba | khturner | 07 October 2014, 14:23:39 UTC | Right Perl script! Whoops. | 07 October 2014, 14:23:39 UTC |
| a6e539a | Keith H. Turner | 07 October 2014, 14:20:42 UTC | Delete TnSeqPileup.pl Whoops! Wrong Perl script. | 07 October 2014, 14:20:42 UTC |
| e158680 | Keith H. Turner | 07 October 2014, 13:26:45 UTC | Update TnSeqDESeqEssential.R Fixed mode calls to be "Reduced" and "Unchanged" so as not to mislead. You still need to check the P-value of your negative binomial test to be sure a gene is Essential. | 07 October 2014, 13:26:45 UTC |
| b3956dc | Keith H. Turner | 23 September 2014, 17:09:36 UTC | Update README.md | 23 September 2014, 17:09:36 UTC |
| 841342c | Keith H. Turner | 23 September 2014, 17:08:58 UTC | Update README.md | 23 September 2014, 17:08:58 UTC |
| d921217 | Keith H. Turner | 23 September 2014, 17:08:46 UTC | Update TnSeqDESeqEssential.R | 23 September 2014, 17:08:46 UTC |
| f705400 | khturner | 23 September 2014, 16:56:00 UTC | Large set of updates associated with latest paper This is an update to nearly all facets of the Tn-seq analysis pipeline. It includes speed improvements in the binning of sites into genes, filtering for reads that include both the amplification primer and the Tn end sequence, and the definition of the differential abundance analysis as an R function, so it can be loaded into RStudio or other IDEs for interactive analyses, figure generation, etc. It also includes the new essential genes analysis, to be described in a new paper shortly. | 23 September 2014, 16:56:04 UTC |
| 3c46ce6 | Keith H. Turner | 14 August 2014, 11:48:04 UTC | Update README.md | 14 August 2014, 11:48:04 UTC |
| 76b9e1d | khturner | 14 August 2014, 11:45:13 UTC | Latest tinkering Added support for more standard annotations in TnSeqDESeq.R (see comments). Also added support for specifying number of mismatches in searching for key sequences. | 14 August 2014, 11:45:13 UTC |
| 23c3b1f | Keith H. Turner | 09 January 2014, 21:47:01 UTC | Update README.md Minor update | 09 January 2014, 21:47:01 UTC |
| 299a78f | Keith H. Turner | 09 January 2014, 21:46:20 UTC | Update TnSeq.sh Added read trimming step to match TnSeq2.sh | 09 January 2014, 21:46:20 UTC |
| 833ea46 | Keith H. Turner | 09 January 2014, 21:41:21 UTC | Update README.md More errors | 09 January 2014, 21:41:21 UTC |
| c7bc447 | Keith H. Turner | 09 January 2014, 21:23:12 UTC | Update README.md Typos | 09 January 2014, 21:23:12 UTC |
| c132540 | khturner | 09 January 2014, 21:13:31 UTC | Competing documentation Added license and readme, and updated documentation for everything | 09 January 2014, 21:13:31 UTC |
| 67bbcb7 | khturner | 05 December 2013, 18:01:03 UTC | Initial commit Uploading analysis resources | 05 December 2013, 18:01:03 UTC |
