Update output.md

nf-core · Feb 29, 2024 · 5625102 · 5625102
1 parent 8fbdef9
commit 5625102
Showing 1 changed file with 43 additions and 101 deletions.
diff --git a/docs/output.md b/docs/output.md
@@ -41,7 +41,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - `<sample_identifier>/`
   - `fastq/`
     - `trimmed_nanofilt/`
-      - `*_filtered.fastq.gz`
+      - `*_filtered.fastq.gz`: The post-trimmed fastq. By default this will be mostly quality trimmed.
 
 </details>
 
@@ -54,10 +54,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - `<sample_identifier>/`
   - `blaze/`
-    - `blaze/*.bc_count.txt`
-    - `blaze/*.knee_plot.png`
-    - `blaze/*.putative_bc.csv`
-    - `blaze/*.whitelist.csv`
+    - `blaze/*.bc_count.txt` : This is a file containing each barcode and the counts of how many reads support it.
+    - `blaze/*.knee_plot.png` : The knee plot detailing the ranking of each barcode.
+    - `blaze/*.putative_bc.csv` : This file contains the naively detected barcode for each read.
+    - `blaze/*.whitelist.csv` : This is the detected "true" barcodes for the dataset.
 
 </details>
 
@@ -74,8 +74,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - `<sample_identifier>/`
   - `bam/`
     - `original/`
-      - `*.sorted.bam`
-      - `*.sorted.bam.bai`
+      - `*.sorted.bam` : The mapped and sorted bam.
+      - `*.sorted.bam.bai` : The bam index for the mapped and sorted bam.
 </details>
 
 [Minimap2](https://github.com/lh3/minimap2) is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Minimap2 is optimized for large, noisy reads making it a staple for alignment of nanopore reads
@@ -88,26 +88,26 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - `<sample_identifier>/`
   - `bam/`
     - `mapped_only/`
-      - `*.sorted.bam`
-      - `*.sorted.bam.bai`
+      - `*.sorted.bam` : The bam contaning only reads that were able to be mapped.
+      - `*.sorted.bam.bai` : The bam index for the bam containing only reads that were able to be mapped.
   - `qc/`
     - `samtools/`
       - `minimap/`
-        - `*.minimap.flagstat`
-        - `*.minimap.idxstats`
-        - `*.minimap.stats`
+        - `*.minimap.flagstat` : The flagstat file for the bam obtained from minimap.
+        - `*.minimap.idxstats` : The idxstats file for the bam obtained from minimap.
+        - `*.minimap.stats` : The stats file for the bam obtained from minimap.
       - `mapped_only/`
-        - `*.mapped_only.flagstat`
-        - `*.mapped_only.idxstats`
-        - `*.mapped_only.stats`
+        - `*.mapped_only.flagstat` : The flagstat file for the bam containing only mapped reads.
+        - `*.mapped_only.idxstats` : The idxstats file for the bam containing only mapped reads.
+        - `*.mapped_only.stats` : The stats file for the bam containing only mapped reads.
       - `corrected/`
-        - `*.corrected.flagstat`
-        - `*.corrected.idxstats`
-        - `*.corrected.stats`
+        - `*.corrected.flagstat` : The flagstat file for the bam containing corrected barcodes.
+        - `*.corrected.idxstats` : The idxstat file for the bam containing corrected barcodes.
+        - `*.corrected.stats` : The stat file for the bam containing corrected barcodes.
       - `dedup/`
-        - `*.dedup.flagstat`
-        - `*.dedup.idxstats`
-        - `*.dedup.stats`
+        - `*.dedup.flagstat` : The flagstat file for the bam containing deduplicated umis.
+        - `*.dedup.idxstats` : The idxstats file for the bam containing deduplicated umis.
+        - `*.dedup.stats` : The stats file for the bam containing deduplicated umis.
 </details>
 
 ![MultiQC - samtools idxstats](images/samtools_idxstats.png)
@@ -122,8 +122,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - `<sample_identifier>/`
   - `bam/`
     - `corrected/`
-      - `*.corrected.bam`
-      - `*.corected.bam.bai`
+      - `*.corrected.bam` : The bam containing corrected barcodes.
+      - `*.corected.bam.bai` : The bam index for the bam containing corrected barcodes.
 
 </details>
 
@@ -136,8 +136,8 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 - `<sample_identifier>/`
   - `bam/`
     - `dedup/`
-      - `*.dedup.bam`
-      - `*.dedup.bam.bai`
+      - `*.dedup.bam` : The bam containing corrected barcodes and deduplicated umis.
+      - `*.dedup.bam.bai` : The bam index for the bam containing corrected barcodes and deduplicated umis.
 
 </details>
 
@@ -152,8 +152,8 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 
 - `<sample_identifier>/`
   - `isoquant/`
-    - `*.gene_counts.tsv`
-    - `*.transcript_counts.tsv`
+    - `*.gene_counts.tsv` : The feature-barcode matrix from gene quantification.
+    - `*.transcript_counts.tsv` : The feature-barcode matrix from transcript quantification.
 
 </details>
 
@@ -166,11 +166,11 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 - `<sample_identifier>/`
   - `qc/`
     - `gene/`
-      - `*.csv`
-      - `*.png`
+      - `*.csv`: A file containing statistics about the cell-read distribution for genes.
+      - `*.png`: A series of qc images to determine the quality of the gene quantification.
     - `transcript/`
-      - `*.csv`
-      - `*.png`
+      - `*.csv`: A file containing statistics about the cell-read distribution for transcript.
+      - `*.png`: A series of qc images to determine the quality of the transcript quantification.
 </details>
 
 ![MultiQC - seurat](images/samtools_idxstats.png)
@@ -214,38 +214,11 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 
 - `batch_qcs/`
   - `nanocomp/`
-    - `fastq/`
-      - `NanoComp_*.log`
-      - `NanoComp_lengths_violin.html`
-      - `NanoComp_log_length_violin.html`
-      - `NanoComp_N50.html`
-      - `NanoComp_number_of_reads.html`
-      - `NanoComp_OverlayHistogram.html`
-      - `NanoComp_OverlayHistogram_Normalized.html`
-      - `NanoComp_OverlayLogHistogram.html`
-      - `NanoComp_OverlayLogHistogram_Normalized.html`
-      - `NanoComp_quals_violin.html`
-      - `NanoComp-report.html`
-      - `NanoComp_total_throughput.html`
-      - `NanoStats.txt`
-    - `bam/`
-      - `NanoComp_20240212_1942.log`
-      - `NanoComp_lengths_violin.html`
-      - `NanoComp_log_length_violin.html`
-      - `NanoComp_N50.html`
-      - `NanoComp_number_of_reads.html`
-      - `NanoComp_OverlayHistogram.html`
-      - `NanoComp_OverlayHistogram_Identity.html`
-      - `NanoComp_OverlayHistogram_Normalized.html`
-      - `NanoComp_OverlayHistogram_PhredScore.html`
-      - `NanoComp_OverlayLogHistogram.html`
-      - `NanoComp_OverlayLogHistogram_Normalized.html`
-      - `NanoComp_percentIdentity_violin.html`
-      - `NanoComp_quals_violin.html`
-      - `NanoComp-report.html`
-      - `NanoComp_total_throughput.html`
-      - `NanoStats.txt`
-
+    - `fastq/` and `bam/`
+      - `NanoComp_*.log`: This is the log file detailing the nanocomp run.
+      - `NanoComp-report.html` - This is browser-viewable report that contains all the figures in a single location.
+      - `*.html`: Nanocomp outputs all the figures in the report as individual files that can be inspected separately.
+      - `NanoStats.txt`: This file contains quality control statistics about the dataset.
 
 </details>
 
@@ -261,43 +234,12 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 - `<sample_identifier>/`
   - `qc/`
     - `nanoplot/`
-      - `pre_trim/`
-        - `LengthvsQualityScatterPlot_dot.html`
-        - `LengthvsQualityScatterPlot_kde.html`
-        - `NanoPlot_20240212_1033.log`
-        - `NanoPlot-report.html`
-        - `NanoStats_post_filtering.txt`
-        - `NanoStats.txt`
-        - `Non_weightedHistogramReadlength.html`
-        - `Non_weightedLogTransformed_HistogramReadlength.html`
-        - `WeightedHistogramReadlength.html`
-        - `WeightedLogTransformed_HistogramReadlength.html`
-        - `Yield_By_Length.html`
-      - `post_trim/`
-        - `LengthvsQualityScatterPlot_dot.html`
-        - `LengthvsQualityScatterPlot_kde.html`
-        - `NanoPlot_20240212_1033.log`
-        - `NanoPlot-report.html`
-        - `NanoStats_post_filtering.txt`
-        - `NanoStats.txt`
-        - `Non_weightedHistogramReadlength.html`
-        - `Non_weightedLogTransformed_HistogramReadlength.html`
-        - `WeightedHistogramReadlength.html`
-        - `WeightedLogTransformed_HistogramReadlength.html`
-        - `Yield_By_Length.html`
-      - `post_extract/`
-        - `LengthvsQualityScatterPlot_dot.html`
-        - `LengthvsQualityScatterPlot_kde.html`
-        - `NanoPlot_20240212_1033.log`
-        - `NanoPlot-report.html`
-        - `NanoStats_post_filtering.txt`
-        - `NanoStats.txt`
-        - `Non_weightedHistogramReadlength.html`
-        - `Non_weightedLogTransformed_HistogramReadlength.html`
-        - `WeightedHistogramReadlength.html`
-        - `WeightedLogTransformed_HistogramReadlength.html`
-        - `Yield_By_Length.html`
-
+      - `pre_trim/` and `post_trim/` and `post_extract`
+        - `NanoPlot_*.log`: This is the log file detailing the nanoplot run
+        - `NanoPlot-report.html` - This is browser-viewable report that contains all the figures in a single location.
+        - `*.html`: Nanoplot outputs all the figures in the report as individual files that can be inspected separately.
+        - `NanoStats.txt`: This file contains quality control statistics about the dataset.
+        - `NanoStats_post_filtering.txt`: If any filtering metrics are used for nanoplot this will contain the differences. This is produced by default and should contain no differences from `NanoStats.txt` if the process was unmodified
 
 </details>
 
@@ -314,7 +256,7 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 - `<sample_identifier>/`
   - `qc/`
     - `rseqc/`
-      - `*.read_distribution.txt`
+      - `*.read_distribution.txt`: This file contains statisitics noting the type of reads located within the dataset
 
 </details>