Last updated: 2020-04-24
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Knit directory: BgeeCall_practical/
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4 RNA-Seq libraries of Drosophila melanogaster just arrived in your RStudio cloud project.
All data you need are stored in the input_files directory at the root of your project.
You and your virtual colleague have one hour to analyse these data and escape the Zoom room.
Generate present/absent expression calls for the RNA-Seq library SRX109273.
Examples of R commands are available in the page One library
Explanations of BgeeCall classes and their most important slots are available in the page BgeeCall classes
Important information :
D. melanogaster NCBI ID : 7227
GTF gene annotations file and fasta transcriptome file are in the directory input_files/ensembl
fastq files are in the directory input_files/fastq/SRX109273/
Even if the generation of kallisto index takes time, you can still manage to escape the Zoom room on time.
Generate present/absent expression calls for the libraries SRX109272 using a file as input R commands and explanation of columns of the file are available in the page List of libraries Explanation of BgeeCall classes and their most important slots are available in the page BgeeCall classes
Important information :
A template of the tsv (Tabular Separated Values) file is available at input_files/inputFile.tsv. You can edit it in RStudio with the function file.edit(“PATH_TO_FILE”) or in the terminal. This file already contains information to run BgeeCall for library SRX109273 (exercice 1). You can keep these information and run BgeeCall for 2 libraries or remove them and run BgeeCall only for library SRX109272.
fastq files of library SRX109272 are in the directory input_files/fastq/SRX109272/
Do not forget to provide the same working_path than in Exercice 1 in order to use previously generated kallisto index
Information about the cutoff for this library are available at YOUR_OUTPUT_DIR/gene_cutoff_info_file.tsv
Fortunatly your collaborator worked well and run BgeeCall on the 2 remaining libraries. She even merged TPM values of the 4 libraries in one file where rows correspond to genes and columns correspond to libraries.
More importantly, she only kept in this file genes considered as present in the 4 libraries.
Everything is ready for downstream analysis. She is now counting on you to do a PCA on these data
Important information :
The file generated by your collaborator is available at input_files/downstream_analysis/present_TPMs.tsv The code to run the PCA is described in the page Processing data
Once more your collaborator was extremely productive. She merged raw counts of the 4 libraries in one file where rows correspond to genes and columns correspond to libraries.
More importantly, she only kept in this file genes considered as present in the 4 libraries.
She is now counting on you to do a differential expression analysis on these data.
Important information :
The file generated by your collaborator is available at input_files/downstream_analysis/present_counts.tsv The code to run the Differential expression is described in the page Processing data
Congratulations!!!! You managed to escape the Zoom room on time. Your collaborator is extremely proud of you.
If you are never full of data analysis you can run a geneset enrichment analysis to have more information on gene differentially expressed