Re-ran denoising script

gerverska · Feb 2, 2023 · 932e282 · 932e282
1 parent c8aaee7
commit 932e282
Show file tree

Hide file tree

Showing 17 changed files with 656 additions and 665 deletions.
diff --git a/03-denoise/logs/fun-frameshift.png → 03-denoise/fun-frameshift.png b/03-denoise/logs/fun-frameshift.png → 03-denoise/fun-frameshift.png
diff --git a/03-denoise/fun-frameshift.rds b/03-denoise/fun-frameshift.rds
diff --git a/03-denoise/logs/gi-frameshift.png → 03-denoise/gi-frameshift.png b/03-denoise/logs/gi-frameshift.png → 03-denoise/gi-frameshift.png
diff --git a/03-denoise/gi-frameshift.rds b/03-denoise/gi-frameshift.rds
diff --git a/03-denoise/logs/filt-R1.html b/03-denoise/logs/filt-R1.html
diff --git a/03-denoise/logs/filt-R1_data/multiqc.log b/03-denoise/logs/filt-R1_data/multiqc.log
diff --git a/03-denoise/logs/filt-R1_data/multiqc_data.json b/03-denoise/logs/filt-R1_data/multiqc_data.json
@@ -421622,14 +421622,14 @@
         "scratch/P01-02-D-n04_fun_fwd-n04_fun_rev-rc-R1_fastqc.zip",
         "scratch/P01-02-D-n07_gi_fwd-n07_gi_rev-rc-R1_fastqc.zip"
     ],
-    "config_creation_date": "2023-01-29, 13:05 PST",
-    "config_git_hash": "b3eb998db8dbde5ab012ccdae3594f6397c264c9",
+    "config_creation_date": "2023-02-02, 13:32 PST",
+    "config_git_hash": "c8aaee74bdf44df633e3342517af9a8bbc09fb18",
     "config_intro_text": null,
     "config_report_comment": null,
     "config_report_header_info": null,
     "config_script_path": "/nfs1/BPP/Spatafora_Lab/gerversk/projects/fun-gi/env/lib/python3.10/site-packages/multiqc/utils",
     "config_short_version": "1.13",
     "config_subtitle": null,
     "config_title": "Forward reads after quality filtering and trimming",
-    "config_version": "1.13 (b3eb998)"
+    "config_version": "1.13 (c8aaee7)"
 }
diff --git a/03-denoise/logs/filt-R2.html b/03-denoise/logs/filt-R2.html
diff --git a/03-denoise/logs/filt-R2_data/multiqc.log b/03-denoise/logs/filt-R2_data/multiqc.log
diff --git a/03-denoise/logs/filt-R2_data/multiqc_data.json b/03-denoise/logs/filt-R2_data/multiqc_data.json
@@ -424978,14 +424978,14 @@
         "scratch/P01-02-D-n04_fun_fwd-n04_fun_rev-rc-R2_fastqc.zip",
         "scratch/P01-02-D-n07_gi_fwd-n07_gi_rev-rc-R2_fastqc.zip"
     ],
-    "config_creation_date": "2023-01-29, 13:06 PST",
-    "config_git_hash": "b3eb998db8dbde5ab012ccdae3594f6397c264c9",
+    "config_creation_date": "2023-02-02, 13:32 PST",
+    "config_git_hash": "c8aaee74bdf44df633e3342517af9a8bbc09fb18",
     "config_intro_text": null,
     "config_report_comment": null,
     "config_report_header_info": null,
     "config_script_path": "/nfs1/BPP/Spatafora_Lab/gerversk/projects/fun-gi/env/lib/python3.10/site-packages/multiqc/utils",
     "config_short_version": "1.13",
     "config_subtitle": null,
     "config_title": "Reverse reads after quality filtering and trimming",
-    "config_version": "1.13 (b3eb998)"
+    "config_version": "1.13 (c8aaee7)"
 }
diff --git a/03-denoise/logs/fun-error-fwd.rds b/03-denoise/logs/fun-error-fwd.rds
diff --git a/03-denoise/logs/fun-error-rev.rds b/03-denoise/logs/fun-error-rev.rds
diff --git a/03-denoise/logs/fun-indel.txt b/03-denoise/logs/fun-indel.txt
@@ -1,7 +1,2 @@
-69735 / 70697
-Fun-trimmed reads
-correctly demultiplexed
-
-102 reads with deletions in N03-N03
-14 reads with insertions in N06-N06
-
+primers total correct deletions insertions
+Fun 70697 69735 102 14
diff --git a/03-denoise/logs/gi-error-fwd.rds b/03-denoise/logs/gi-error-fwd.rds
diff --git a/03-denoise/logs/gi-error-rev.rds b/03-denoise/logs/gi-error-rev.rds
diff --git a/03-denoise/logs/gi-indel.txt b/03-denoise/logs/gi-indel.txt
@@ -1,7 +1,2 @@
-14283 / 15477
-Gi-trimmed reads
-correctly demultiplexed
-
-203 reads with deletions in N06-N06
-17 reads with insertions in N09-N09
-
+primers total correct deletions insertions
+Gi 15477 14283 203 17
diff --git a/code/03-denoise.r b/code/03-denoise.r
@@ -34,6 +34,7 @@ out <- '03-denoise'
 logs <- file.path(out, 'logs')
 unlink(out, recursive = T)
 dir.create(logs, recursive = T)
+dir.create('scratch')
 system(paste('touch', file.path(out, 'README.md')))
 
 # Read in forward and reverse reads ####
@@ -84,4 +85,4 @@ denoise(marker = 'fun')
 denoise(marker = 'gi')
 
 # Remove the scratch directory ####
-unlink('scratch', recursive = T)
+unlink('scratch', recursive = T)