diff --git a/bu_isciii/assets/reports/md/rnaseq.md b/bu_isciii/assets/reports/md/rnaseq_deg.md similarity index 99% rename from bu_isciii/assets/reports/md/rnaseq.md rename to bu_isciii/assets/reports/md/rnaseq_deg.md index 3a753d32..c3157323 100755 --- a/bu_isciii/assets/reports/md/rnaseq.md +++ b/bu_isciii/assets/reports/md/rnaseq_deg.md @@ -1,7 +1,7 @@ -# mRNAseq: Output +# mRNAseq (DEG): Output ## Introduction diff --git a/bu_isciii/assets/reports/results/rnaseq.md b/bu_isciii/assets/reports/results/rnaseq_deg.md similarity index 86% rename from bu_isciii/assets/reports/results/rnaseq.md rename to bu_isciii/assets/reports/results/rnaseq_deg.md index c5cb919d..8c39926f 100644 --- a/bu_isciii/assets/reports/results/rnaseq.md +++ b/bu_isciii/assets/reports/results/rnaseq_deg.md @@ -1,25 +1,27 @@ -## mRNAseq +# mRNAseq (DEG): results Here we describe the results from the mRNAseq pipeline for transcriptomic analysis and differential gene expression. > [!WARNING] > Some of the files listed here may not be in your `RESULTS` folder. It will depend on the analysis you requested. -### Alignment and quantification +## Alignment and quantification -> [!WARNING]: Please note that the files in the RESULTS directory are still pending determination by our administrative team. We are currently discussing which generic/common files will be included in this section to ensure that you receive the most relevant and useful information for your analysis. +> [!WARNING] +> Please note that the files in the RESULTS directory are still pending determination by our administrative team. We are currently discussing which generic/common files will be included in this section to ensure that you receive the most relevant and useful information for your analysis. -### Differential expression analysis with DESEQ2 +## Differential expression analysis with DESEQ2 -> [!WARNING]: Please note that the files in the RESULTS directory are still pending determination by our administrative team. We are currently discussing which generic/common files will be included in this section to ensure that you receive the most relevant and useful information for your analysis. +> [!WARNING] +> Please note that the files in the RESULTS directory are still pending determination by our administrative team. We are currently discussing which generic/common files will be included in this section to ensure that you receive the most relevant and useful information for your analysis. -### Interpretation of Differential Expression Results: +## Interpretation of Differential Expression Results: For each comparison conducted, a separate folder has been created, following the naming convention outlined below: @@ -38,7 +40,7 @@ Additionally, the file `normalized_expression.xlsx` contains the normalized expr > [!WARNING] > Software's versions used in this analysis can be obtained from the `MultiQC` report. -#### Description of output files +### Description of output files - `/Differential_expression/DESeq2/Differential_expression.csv`: This file contains the results of the differential expression analysis performed using DESeq2, including information on differentially expressed genes and associated statistical metrics such as fold change, p-values, and adjusted p-values. - `/Differential_expression/DESeq2/heatmapCount_top20_differentially_expressed.pdf`: This PDF file presents a heatmap visualization displaying the expression patterns of the top 20 differentially expressed genes, clustered by sample distance, as determined by the DESeq2 analysis. diff --git a/bu_isciii/templates/services.json b/bu_isciii/templates/services.json index a21e7803..a664e842 100755 --- a/bu_isciii/templates/services.json +++ b/bu_isciii/templates/services.json @@ -150,8 +150,8 @@ }, "no_copy": ["RAW", "TMP"], "last_folder":"RESULTS", - "delivery_md": "assets/reports/md/rnaseq.md", - "results_md": "assets/reports/results/rnaseq.md" + "delivery_md": "assets/reports/md/rnaseq_deg.md", + "results_md": "assets/reports/results/rnaseq_deg.md" }, "lowfreq_panel": { "label": "",