Skip to content

Commit 3d32ab4

Browse files
XinpeiYiXinpeiYi
committed
DeepRescore2 update!
1 parent e1d673a commit 3d32ab4

10 files changed

+2
-13
lines changed

‎DeepRescore2/Parameters/PXD000138_maxquant.param

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,6 @@ DeepRescore2Path E:/Project/DeepRescore2/test2/DeepRescore2/DeepRescore2
33
anacondaPath /C/ProgramData/anaconda3
44
decoyPrefix XXX_
55
searchEngine maxquant
6-
inputPath E:/Project/DeepRescore2/test2/ExampleData1/PXD000138
76
rawSpectraPath E:/Project/DeepRescore2/test2/ExampleData1/PXD000138/RAW
87
spectraPath E:/Project/DeepRescore2/test2/ExampleData1/PXD000138/MGF
98
inputFeaturePath E:/Project/DeepRescore2/test2/ExampleData1/PXD000138/features_maxquant.txt

‎DeepRescore2/Parameters/PXD023665_comet.param

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,6 @@ DeepRescore2Path E:/Project/DeepRescore2/test2/DeepRescore2/DeepRescore2
33
anacondaPath /C/ProgramData/anaconda3
44
decoyPrefix REV_
55
searchEngine comet
6-
inputPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665
76
rawSpectraPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/RAW
87
spectraPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/MGF
98
inputFeaturePath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/features_comet.txt

‎DeepRescore2/Parameters/PXD023665_maxquant.param

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,6 @@ DeepRescore2Path E:/Project/DeepRescore2/test2/DeepRescore2/DeepRescore2
33
anacondaPath /C/ProgramData/anaconda3
44
decoyPrefix XXX_
55
searchEngine maxquant
6-
inputPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665
76
rawSpectraPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/RAW
87
spectraPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/MGF
98
inputFeaturePath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/features_maxquant.txt

‎DeepRescore2/Parameters/PXD023665_msgf.param

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,6 @@ DeepRescore2Path E:/Project/DeepRescore2/test2/DeepRescore2/DeepRescore2
33
anacondaPath /C/ProgramData/anaconda3
44
decoyPrefix REV_
55
searchEngine msgf
6-
inputPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665
76
rawSpectraPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/RAW
87
spectraPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/MGF
98
inputFeaturePath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/features_msgf.txt

‎DeepRescore2/Parameters/PXD023665_xtandem.param

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,6 @@ DeepRescore2Path E:/Project/DeepRescore2/test2/DeepRescore2/DeepRescore2
33
anacondaPath /C/ProgramData/anaconda3
44
decoyPrefix REV_
55
searchEngine xtandem
6-
inputPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665
76
rawSpectraPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/RAW
87
spectraPath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/MGF
98
inputFeaturePath E:/Project/DeepRescore2/test2/ExampleData2/PXD023665/features_xtandem.txt

‎DeepRescore2/Parameters/UCEC_comet.param

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,6 @@ DeepRescore2Path E:/Project/DeepRescore2/test2/DeepRescore2/DeepRescore2
33
anacondaPath /C/ProgramData/anaconda3
44
decoyPrefix REV_
55
searchEngine comet
6-
inputPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC
76
rawSpectraPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/RAW
87
spectraPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/MGF
98
inputFeaturePath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/features_comet.txt

‎DeepRescore2/Parameters/UCEC_maxquant.param

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,7 @@ Name Value
22
DeepRescore2Path E:/Project/DeepRescore2/test2/DeepRescore2/DeepRescore2
33
anacondaPath /C/ProgramData/anaconda3
44
decoyPrefix XXX_
5-
searchEngine maxquant
6-
inputPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC
5+
searchEngine maxquants
76
rawSpectraPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/RAW
87
spectraPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/MGF
98
inputFeaturePath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/features_maxquant.txt

‎DeepRescore2/Parameters/UCEC_msgf.param

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,6 @@ DeepRescore2Path E:/Project/DeepRescore2/test2/DeepRescore2/DeepRescore2
33
anacondaPath /C/ProgramData/anaconda3
44
decoyPrefix REV_
55
searchEngine msgf
6-
inputPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC
76
rawSpectraPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/RAW
87
spectraPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/MGF
98
inputFeaturePath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/features_msgf.txt

‎DeepRescore2/Parameters/UCEC_xtandem.param

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,6 @@ DeepRescore2Path E:/Project/DeepRescore2/test2/DeepRescore2/DeepRescore2
33
anacondaPath /C/ProgramData/anaconda3
44
decoyPrefix REV_
55
searchEngine xtandem
6-
inputPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC
76
rawSpectraPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/RAW
87
spectraPath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/MGF
98
inputFeaturePath E:/Project/DeepRescore2/test2/ExampleData3/UCEC/features_xtandem.txt

‎README.md

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -105,8 +105,7 @@ $ mv SpectralEntropy DeepRescore2/Script/pDeep3
105105
$ cd DeepRescore2
106106
$ ./Install/Install.sh . $AnacondaPath
107107
```
108-
**After installation, please double check whether AutoRT, pDeep3 and R_env conda environments is exist under the Anaconda environment folder (default is in C:\ProgramData\anaconda3\envs) or not.**
109-
108+
**After installation, please verify whether the AutoRT, pDeep3, and R_env conda environments exist in the Anaconda environment folder (typically located at C:\ProgramData\anaconda3\envs) or not.**
110109

111110
### Data type
112111
- Instrument Type: The proposed approach, DeepRescore2, is designed to be applicable to mass spectrometry-based proteomics data obtained from various types of instruments, including but not limited to Orbitrap, Q-TOF, and ion trap instruments.
@@ -272,7 +271,6 @@ Each column of the parameter file is described as follows (Please change the 'Va
272271
| anacondaPath | ANACONDA_DIR | Anaconda directory. Default is /C/ProgramData/anaconda3 |
273272
| decoyPrefix | DECOY_PREFIX | Decoy prefix used for searching. Default is XXX_ |
274273
| searchEngine | SEARCH_ENGINE | Four search engines, msgf, comet, xtandem, maxquant, are supported |
275-
| inputPath | INPUT_DIR | Input directory including all the input files |
276274
| rawSpectraPath | RAW_DIR | Path to the MS/MS spectra (RAW) directory |
277275
| spectraPath | MGF_DIR | Path to the MS/MS spectra (MGF) directory |
278276
| inputFeaturePath | FEATURE_DIR | Path to the feature matrix |

0 commit comments

Comments
 (0)