Commits · 465e6e9036a8e71e31e52d577d72d110582291c4 · Matej Lexa / hic-te

Sep 07, 2021
- Fixed a typo in calling intersect_bed (missing t) · 465e6e90
  Matej Lexa authored Sep 07, 2021
  
  465e6e90
Sep 06, 2021
- added few comments · ac325e59
  Monika Čechová authored Sep 06, 2021
  
  ac325e59
- pairs of families that are significant are now written into the file · 76e13898
  Monika Čechová authored Sep 06, 2021
  
  76e13898
- rename to match the agreed format of the .tab file; limit the circos plots to 500 lines per plot · 1850f506
  Monika Čechová authored Sep 06, 2021
  
  1850f506
- create the index of the genome only if it does not exist yet · 2844dd37
  Monika Čechová authored Sep 06, 2021
  
  2844dd37
- Update circos.nf · caa63315
  Monika Čechová authored Sep 06, 2021
  
  caa63315
Sep 05, 2021
- Fixed an error of shuffling also experimental dataset that should have stayed unshuffled · 80bbb63a
  Matej Lexa authored Sep 05, 2021
  
  80bbb63a
- Convert 'TE to heatmap' to dsl2, add modules · 82c97d7e
  Son Hoang Nguyen authored Sep 05, 2021
  
  82c97d7e
Sep 02, 2021
- Update test.config · a942a859
  Son Hoang Nguyen authored Sep 02, 2021
  
  a942a859
- Add test profile, update main_TE_combined.nf with skip parameters · eee446e5
  Son Hoang Nguyen authored Sep 02, 2021
  
  eee446e5
- Modified ggplot calls to show title and axis labels · f7ce1b60
  Matej Lexa authored Sep 02, 2021
  
  f7ce1b60
- Added all steps of shuffledNormalization (bash + R) · 96a849e9
  Matej Lexa authored Sep 02, 2021
  
  96a849e9
- Fixed a bug when input contained an empty annot= variable · 5870c1df
  Matej Lexa authored Sep 02, 2021
  
  5870c1df
Sep 01, 2021
- adjusted regex in script to new tab format produced by extract_pairs.pl · 2f23f45b
  Matej Lexa authored Sep 01, 2021
  
  2f23f45b
- A format converter based on rtracklayer · 0b5a30ac
  Matej Lexa authored Sep 01, 2021
  
  0b5a30ac
- Changed pipeline to reflect changes in extract_pairs.pl · b719c2e0
  Matej Lexa authored Sep 01, 2021
  
  b719c2e0
- Adapted script to the new table format produced by extract_pairs.pl · d92dc881
  Matej Lexa authored Sep 01, 2021
  
  d92dc881
- Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/hic-te · a2e98ce0
  Matej Lexa authored Sep 01, 2021
  
  a2e98ce0
- Modified script to produce a leaner table and accept distance limits · 7314c81c
  Matej Lexa authored Sep 01, 2021
  
  7314c81c
- Update plot_family_pairs.R · f3391ebc
  Monika Čechová authored Sep 01, 2021
  
  f3391ebc
- add process for the generation of genome file · c27cde37
  Monika Čechová authored Sep 01, 2021
  
  c27cde37
- automatically generate genome file for circos plots · 283275ba
  Monika Čechová authored Sep 01, 2021
  
  283275ba
- specify number of output reads · 5a96f915
  Monika Čechová authored Sep 01, 2021
  
  5a96f915
- specify number of output reads · fff1945a
  Monika Čechová authored Sep 01, 2021
  
  fff1945a
- Initial commit of new R script · dcc612da
  Matej Lexa authored Sep 01, 2021
  
  dcc612da
- Changed number of repetitions for random annotation · 70771fe7
  Matej Lexa authored Sep 01, 2021
  
  70771fe7
Aug 31, 2021
- Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/hic-te · 27e1b2cc
  Matej Lexa authored Aug 31, 2021
  
  27e1b2cc
- A set of scripts to generate random intervals for testing for a given reference genome · c5c6c851
  Matej Lexa authored Aug 31, 2021
  
  c5c6c851
- Add new file · 89c87d23
  Monika Čechová authored Aug 31, 2021
  
  89c87d23
- Added three more types of heatmaps (all, tad, dist) to the output · 230ed574
  Matej Lexa authored Aug 31, 2021
  
  230ed574
- Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/hic-te · fa079bae
  Matej Lexa authored Aug 31, 2021
  
  fa079bae
- fixed annotation · 4e077898
  Matej Lexa authored Aug 31, 2021
  
  4e077898
- Add new file · f9ca4d82
  Monika Čechová authored Aug 31, 2021
  
  f9ca4d82
Aug 28, 2021
- Fixed a bug where some lines were not pushed to @oldlines1/2; also a typo in... · 2b4735d7
  Matej Lexa authored Aug 28, 2021
```
Fixed a bug where some lines were not pushed to @oldlines1/2; also a typo in undef @oldlines2 that messed up the output
```
  2b4735d7
- A perl script to carry out local sorting and duplicate elimination after... · a52e6134
  Matej Lexa authored Aug 28, 2021
```
A perl script to carry out local sorting and duplicate elimination after bedtool intersect and pair formation for tabulation
```
  a52e6134
Aug 27, 2021
- Fixed a bug in extract_pairs.pl that assumed HiC read pairs only connect... · 15297878
  Matej Lexa authored Aug 27, 2021
```
Fixed a bug in extract_pairs.pl that assumed HiC read pairs only connect (bedtools intersect) two annotations and not more
```
  15297878
- Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/hic-te · 8a581d95
  Matej Lexa authored Aug 27, 2021
  
  8a581d95
- A suggestion for fixing a bug with reference headers containing space · c5643ad7
  Matej Lexa authored Aug 27, 2021
  
  c5643ad7
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

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