This repository contains the code used to carry out the final master project titled: RNA sequencing role in the genetic diagnosis of hereditary breast and ovarian cancer
Here is the workflow followed in the project:
Comparison of TPM values between our study and those obtained from GTEx. The code is located in the R folder under the name .
The first step was to run the RNA-seq pipeline using Nextflow. To achieve this:
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We created a nextflow.config file, located in the BASH folder under the name
. This file contains the Nextflow requirements for job distribution and resource allocation.
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We created a shell script with the necessary specifications to run the nf-core pipeline, located in the BASH folder under the name
.
The second step was to examine the outputs/results obtained by the pipeline. To achieve this:
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First, we performed a differential expression analysis (DEA). The code is located in the R folder under the name
.
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Second, we performed an analysis to find aberrantly expressed genes in RNA-seq samples. The code is located in the R folder under the name
.
The first step was to run the RNA-splice pipeline using Nextflow. To achieve this:
-
We created a nextflow.config file, located in the BASH folder under the name
. This file contains the Nextflow requirements for job distribution and resource allocation.
-
We created a shell script with the necessary specifications to run the nf-core pipeline, located in the BASH folder under the name
.
The second step was to examine the outputs/results obtained by the pipeline. To achieve this:
-
First, we performed a differential exon usage analysis (DEU). The code is located in the R folder under the name
.
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Second, we processed the .dpsi objects obtained from the SUPPA analysis, which was automatically performed by the pipeline. The code is located in the R folder under the name
.
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Third, we performed an analysis for the detection of aberrant gene expression events in RNA-seq data. The code is located in the R folder under the name
.