Commits · master · Hannes Reinwald / bioinf

27 Dec, 2017 3 commits
- Merge branch 'master' of gitlab.leibniz-zmt.de:chh/bioinf · a99c7108
  Christiane Hassenrueck authored Dec 27, 2017
  
  a99c7108
- adjusted 16S_run_v2.sh for output of latest silvangs version · 78fdf7f8
  Christiane Hassenrueck authored Dec 27, 2017
  
  78fdf7f8
- added taxonomy file for silva version 132 · cb3ecce5
  Christiane Hassenrueck authored Dec 27, 2017
  
  cb3ecce5
27 Nov, 2017 1 commit
- bug fix in taxonomy curation allowing for no chloroplast and mitochondria OTUs · 546fb55a
  Christiane Hassenrueck authored Nov 27, 2017
  
  546fb55a
28 Jul, 2017 2 commits
- bugfix mitochondria removal · c0ccc521
  Christiane Hassenrueck authored Jul 28, 2017
  
  c0ccc521
- bugfix in mitochondria removal · 3c14dd85
  Christiane Hassenrueck authored Jul 28, 2017
  
  3c14dd85
17 Jul, 2017 3 commits
- added +x permission for data_curation_silvangs.R · cebd1fd2
  Christiane Hassenrueck authored Jul 17, 2017
  
  cebd1fd2
- added silvangs as alternative taxonomic classification tool · 7c936ee0
  Christiane Hassenrueck authored Jul 17, 2017
  
  7c936ee0
- revision paprica commands · 33cf779e
  Christiane Hassenrueck authored Jul 17, 2017
  
  33cf779e
28 Jun, 2017 1 commit
- updated dada2_16S.R added pool=T option for dada() · 7dbb9545
  Christiane Hassenrueck authored Jun 28, 2017
  
  7dbb9545
26 Jun, 2017 1 commit
- reading input using data.table package · 937b8b67
  Christiane Hassenrueck authored Jun 26, 2017
  
  937b8b67
02 May, 2017 2 commits
- updated paprica_script.txt · 3b4d81bf
  Christiane Hassenrueck authored May 02, 2017
  
  3b4d81bf
- bugfix in paprica_srun.sh · 20b96947
  Christiane Hassenrueck authored May 02, 2017
  
  20b96947
27 Apr, 2017 1 commit
- added exetuable permissions · 791ac5f5
  Christiane Hassenrueck authored Apr 27, 2017
  
  791ac5f5
24 Apr, 2017 1 commit
- some updates to paprica_script.txt · d2d44da4
  Christiane Hassenrueck authored Apr 24, 2017
  
  d2d44da4
05 Apr, 2017 2 commits
- further development of paprica workflow. still a work in progress · 45b9fa67
  Christiane Hassenrueck authored Apr 05, 2017
  
  45b9fa67
- started on script for metabolic inference using paprica. Still a work in progress. · 2e89e48a
  Christiane Hassenrueck authored Apr 05, 2017
  
  2e89e48a
31 Mar, 2017 1 commit
- added comment on sina usage · 69c6e24c
  Christiane Hassenrueck authored Mar 31, 2017
  
  69c6e24c
27 Mar, 2017 1 commit

more memory for sina and med jobs · f34cce33

Christiane Hassenrueck authored Mar 27, 2017

bugfix in generation of final sina output for med option
added more detailed comments for analysis steps

f34cce33

23 Mar, 2017 2 commits
- reformatting of nSeqs file to tabular output · 63d294d8
  Christiane Hassenrueck authored Mar 23, 2017
  
  63d294d8
- edit srun settings for swarm and med command · 4af085a6
  Christiane Hassenrueck authored Mar 23, 2017
  
  4af085a6
17 Mar, 2017 3 commits
- updates in MED workflow · 7ddb5869
  Christiane Hassenrueck authored Mar 17, 2017
  
  7ddb5869
- bugfix in location of *done file in med_v2.sh · bab5448f
  Christiane Hassenrueck authored Mar 17, 2017
  
  bab5448f
- fixed typo in MED section · 491627c7
  Christiane Hassenrueck authored Mar 17, 2017
  
  491627c7
16 Mar, 2017 1 commit
- Bugfix in setting sequence counter in sina_v2.sh · 3a6a4910
  Christiane Hassenrueck authored Mar 16, 2017
  
  3a6a4910
14 Mar, 2017 3 commits
- added comments on parameter selection for merging and changed overlap and... · df902b4d
  Christiane Hassenrueck authored Mar 14, 2017
```
added comments on parameter selection for merging and changed overlap and mismatch parameter in command
```
  df902b4d
- added alternative master sequencer script for low quality reads or long... · f08fb2a7
  Christiane Hassenrueck authored Mar 14, 2017
```
added alternative master sequencer script for low quality reads or long inserts (merge first, trim later)
```
  f08fb2a7
- added code to shorten file names · 3e7f23f5
  Christiane Hassenrueck authored Mar 14, 2017
  
  3e7f23f5
07 Mar, 2017 2 commits
- included comment on computing resources in dada2_16S.R · 965604f4
  Christiane Hassenrueck authored Mar 07, 2017
  
  965604f4
- added example dada2 script · 1881adcf
  Christiane Hassenrueck authored Mar 07, 2017
  
  1881adcf
03 Mar, 2017 1 commit
- added folder to store images for wiki · 8c3fbacb
  Christiane Hassenrueck authored Mar 03, 2017
  
  8c3fbacb
01 Mar, 2017 2 commits
- fixed typo in generation of fastqc diagnostic files · 2a258c9a
  Christiane Hassenrueck authored Mar 01, 2017
  
  2a258c9a
- added executable permissions · 1fffbb61
  Christiane Hassenrueck authored Mar 01, 2017
  
  1fffbb61
03 Feb, 2017 1 commit
- fixed typos in experimental design presentation · 772d50dc
  Christiane Hassenrueck authored Feb 03, 2017
  
  772d50dc
02 Feb, 2017 1 commit
- Added notes for morning workshop 3.2.2017 · 4005a2ed
  Christiane Hassenrueck authored Feb 02, 2017
  
  4005a2ed
01 Feb, 2017 1 commit
- some bog fixes in generation of diagnostic files and sina. Not tested yet · db2ae678
  Christiane Hassenrueck authored Feb 01, 2017
  
  db2ae678
27 Jan, 2017 1 commit
- bug fix in generation of diagnostic files for QC · 25750e18
  Christiane Hassenrueck authored Jan 27, 2017
  
  25750e18
24 Jan, 2017 1 commit
- Added tutorial scripts and presentations · 9131746f
  Christiane Hassenrueck authored Jan 24, 2017
  
  9131746f
17 Jan, 2017 1 commit
- bug fix in waiting step of med_merge_v2.sh and fasta_merge_v2.sh · ee9da42e
  Christiane Hassenrueck authored Jan 17, 2017
  
  ee9da42e
16 Jan, 2017 1 commit
- Bug fixes in MED step · 0d639282
  Christiane Hassenrueck authored Jan 16, 2017
  
  0d639282