Commits · 92d41ade115b562b0793fad3e780a5e5514b0eab · Matej Lexa / hic-te

Aug 26, 2021
- Fixed typo (.instead of _ in filename) in prepare_fastq_for_RepeatExplorer.sh · 92d41ade
  Matej Lexa authored Aug 26, 2021
  
  92d41ade
Aug 25, 2021

Replaced bwa mem with mapPacBio.sh from BBMap package, added PlantSat sequence... · afca8412

Matej Lexa authored Aug 25, 2021

Replaced bwa mem with mapPacBio.sh from BBMap package, added PlantSat sequence analysis analogically to contigs from Repeat Explorer

afca8412

Aug 22, 2021
- Add new file · fa343923
  Monika Čechová authored Aug 22, 2021
  
  fa343923
- Add new file · 850f981d
  Monika Čechová authored Aug 22, 2021
  
  850f981d
Aug 15, 2021
- Add missing TE_to_heatmap.nf · e391bb58
  Son Hoang Nguyen authored Aug 15, 2021
  
  e391bb58
- 'Merge' from develop · 23642a04
  Son Hoang Nguyen authored Aug 15, 2021
  
  23642a04
Aug 12, 2021
- Temporary nextflow file, to be deleted after circos module is incorporated · c7d1688f
  Monika Čechová authored Aug 12, 2021
  
  c7d1688f
- added module for circos plots · 70ad6d8f
  Monika Čechová authored Aug 12, 2021
  
  70ad6d8f
- Added R code for creating circos plots · 7d9ccbc3
  Monika Čechová authored Aug 12, 2021
  
  7d9ccbc3
Jul 09, 2021
- no renumbering of reads as the RE now uses the -keep_names option · 7d8c7ad5
  Monika Čechová authored Jul 09, 2021
  
  7d8c7ad5
- no renumbering of reads as the RE now uses the -keep_names option · 26c0aae9
  Monika Čechová authored Jul 09, 2021
  
  26c0aae9
- processes now moved to modules, test paired data are read into the channel and... · 69e0954b
  Monika Čechová authored Jul 09, 2021
```
processes now moved to modules, test paired data are read into the channel and passed into the pipeline
```
  69e0954b
- Add new file · 2dc68fa3
  Monika Čechová authored Jul 09, 2021
  
  2dc68fa3
- Add new file · b5cc3986
  Monika Čechová authored Jul 09, 2021
  
  b5cc3986
- Add new directory · 6d1d9231
  Monika Čechová authored Jul 09, 2021
  
  6d1d9231
Jun 29, 2021
- Add new file · 0249dd28
  Monika Čechová authored Jun 29, 2021
  
  0249dd28
- Add new file · eaa95d8a
  Monika Čechová authored Jun 29, 2021
  
  eaa95d8a
- extended the script to include blast results, assignment to clusters, and the... · 8ad0858c
  Monika Čechová authored Jun 29, 2021
```
extended the script to include blast results, assignment to clusters, and the calculation of the matrix
```
  8ad0858c
Jun 25, 2021
- Add new file · ff799dda
  Monika Čechová authored Jun 25, 2021
  
  ff799dda
- Add new file · 23b59bcf
  Monika Čechová authored Jun 25, 2021
  
  23b59bcf
- Add new directory · cc3b5185
  Monika Čechová authored Jun 25, 2021
  
  cc3b5185
- replaced label_reads_by_cluster with the information from hitsort.cls file · 5bfcf991
  Monika Čechová authored Jun 25, 2021
  
  5bfcf991
Jun 18, 2021
- Initial commit for FASTQ preparation scripts so they can be analyzed with Repeat Explorer · 8c6d2c6f
  Matej Lexa authored Jun 18, 2021
  
  8c6d2c6f
Apr 10, 2021
- added a teref_size parameter description to the help page · 9427d823
  Matej Lexa authored Apr 10, 2021
  
  9427d823
- this test version works on adh1 reference now, skipping two key lines in TEref generation script · ea78aeec
  Matej Lexa authored Apr 10, 2021
  
  ea78aeec
- added a branch of processes to run TE-g-nester and generate artificial chromosomes for TE families · 108de874
  Matej Lexa authored Apr 10, 2021
  
  108de874
Apr 09, 2021
- basic functionality there · f0510108
  Matej Lexa authored Apr 09, 2021
  
  f0510108
- adding first imputs and outputs · 5b62ff4a
  Matej Lexa authored Apr 09, 2021
  
  5b62ff4a
- full pipeline draft, testing on Slyc · 7f8d5c70
  Matej Lexa authored Apr 09, 2021
  
  7f8d5c70
- added help message, made sra_run mandatory · 4f3a5cdc
  Matej Lexa authored Apr 09, 2021
  
  4f3a5cdc
- reformatted script and config · 1198a962
  Matej Lexa authored Apr 09, 2021
  
  1198a962
- added .gitignore · e6e54ae6
  Matej Lexa authored Apr 09, 2021
  
  e6e54ae6
- started the hic-te nextflow project · 80f0c2ab
  Matej Lexa authored Apr 09, 2021
  
  80f0c2ab
- Initial commit · 5107a29a
  Matej Lexa authored Apr 09, 2021
  
  5107a29a

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