Commits · 77f8dab4d51ed53200a7371bd3fb5668fa41fda8 · bioinfo / ngs_tools

Jun 01, 2016
- added bioinfo-srv1 compatibility · 5b43501d
  Holger Brandl authored 8 years ago
  
  5b43501d
May 30, 2016
- avoid that _2.fastqs are mapping · 3ce7f8c4
  Holger Brandl authored 8 years ago
  
  3ce7f8c4
May 25, 2016
- switched back to furiosa config · b31b589b
  Holger Brandl authored 8 years ago
  
  b31b589b
- fixed madmax config · ee236d89
  Holger Brandl authored 8 years ago
  
  ee236d89
May 17, 2016
- cosmetics · 92a54c21
  Holger Brandl authored 8 years ago
  
  92a54c21
May 13, 2016
- deseq workflow cosmetics · aea6b362
  Holger Brandl authored 8 years ago
  
  aea6b362
May 12, 2016
- cont mf-deseq · 5b9dc042
  Holger Brandl authored 8 years ago
  
  5b9dc042
- cont furiosa porting of rna-seq workflow · 22279176
  Holger Brandl authored 8 years ago
  
  22279176
- clean up and tool deprecation · 10fdfc65
  Holger Brandl authored 8 years ago
  
  10fdfc65
- improved deseq reporting · a4056b0f
  Holger Brandl authored 8 years ago
  
  a4056b0f
May 11, 2016
- cont. mf deseq · b485c9e1
  Holger Brandl authored 8 years ago
  
  b485c9e1
- cont mf deseq · ffc16c40
  Holger Brandl authored 8 years ago
  
  ffc16c40
May 10, 2016
- started new mf deseq · 2d9c0213
  Holger Brandl authored 8 years ago
  
  2d9c0213
- fixed dependencies · 089f52cb
  Holger Brandl authored 8 years ago
  
  089f52cb
May 09, 2016
- add fpkm export to featcounts_deseq · d3488019
  Holger Brandl authored 8 years ago
  
  d3488019
May 04, 2016
- fixed typo in cleanup section · 398c04b4
  Holger Brandl authored 8 years ago
  
  398c04b4
- fixed memory and walltime · af05af46
  Holger Brandl authored 8 years ago
  
  af05af46
Apr 28, 2016
- more robust fastqc wrapper · 59b6e27e
  Holger Brandl authored 8 years ago
  
  59b6e27e
Apr 08, 2016
- updated bam correlation to work with latest deeptools. @lakshman v2.2.2 of... · 740c4ae0
  Holger Brandl authored 9 years ago
  
  updated bam correlation to work with latest deeptools. @lakshman v2.2.2 of deeptools is required now to run the star-workflow
  740c4ae0
- changed to use ngs_tools master by default · 44ecad36
  Holger Brandl authored 9 years ago
  
  44ecad36
- separated star and b1 workflows · e797a356
  Holger Brandl authored 9 years ago
  
  e797a356
Apr 06, 2016
- refined star workflow · 01b4dab6
  Holger Brandl authored 9 years ago
  
  01b4dab6
Apr 04, 2016
- fixed incorrect wall time · 342c00c5
  Holger Brandl authored 9 years ago
  
  342c00c5
Apr 01, 2016
- improved bash style · 944e014f
  Holger Brandl authored 9 years ago
  
  944e014f
Mar 24, 2016

changed to use more recent version v2.2.2 of deeptools. @lakshman to switch as... · 8fcaca17

Holger Brandl authored 9 years ago

changed to use more recent version v2.2.2 of deeptools. @lakshman to switch as well, you'll need to do a user install for your account first I guess. This is because I cant do a global installation on the cluster.

8fcaca17

Mar 17, 2016
- changed default aligner wrapper to kts-version · b7921c6e
  Holger Brandl authored 9 years ago
  
  b7921c6e
- require existence of fastq inputs · 4189ca94
  Holger Brandl authored 9 years ago
  
  4189ca94
- save cached jar next to script until #5 is fixed. · 8b2eaaaf
  Holger Brandl authored 9 years ago
  
  8b2eaaaf
- added start tests · dc74d040
  Holger Brandl authored 9 years ago
  
  dc74d040
Mar 16, 2016
- rewritten scala utils in kotlin · 6b5fcd52
  Holger Brandl authored 9 years ago
  
  6b5fcd52
Mar 15, 2016
- use latest 2.5.1b STAR · def09006
  Holger Brandl authored 9 years ago
  
  def09006
- improved bash wrapper · b32e2aa7
  Holger Brandl authored 9 years ago
  
  b32e2aa7
- cont pe-aligner wrapper · ad70d502
  Holger Brandl authored 9 years ago
  
  ad70d502
- started pe-aligner wrapper · 53b1a7a1
  Holger Brandl authored 9 years ago
  
  53b1a7a1
Mar 08, 2016
- Problem with plotDispEsts resolved by callign DESeq before and also loaded... · cf9fc936
  Naharajan authored 9 years ago
  
  Problem with plotDispEsts resolved by callign DESeq before and also loaded readr library for write_tsv
  cf9fc936
Mar 02, 2016
- @lakshman fixed failing star report. Now it wont mattter if bc is not yet done. · 936cea09
  Holger Brandl authored 9 years ago
  
  936cea09
- extended gc vs cov analysis · 23ceb568
  Holger Brandl authored 9 years ago
  
  23ceb568
Mar 01, 2016
- disabled chmod when building star index · 9482f08b
  Holger Brandl authored 9 years ago
  
  9482f08b
Feb 29, 2016
- @lakshman disabled chmod when creating star index · adebf72f
  Holger Brandl authored 9 years ago
  
  adebf72f
Feb 26, 2016
- adopted fc dba analysis for new data. · 4c51eecd
  Holger Brandl authored 9 years ago
  
  4c51eecd