amynjaaye / rnaseq

RNAseq

Instructions for analysis

The goal of this analysis is to perform a differential expression analysis at gene level (mRNA isoforms are not taken into account).

The following instructions are short in purpose: additional information or tools can be deduced, or retrieve from public databases.

1. Download 4 sequence datasets deposited to the EBI ENA:

ERR990557

ERR990558

ERR990559

ERR990560

These datasets have been generated in a work published in Embo Reports :

Molla-Herman A, Vallés AM, Ganem-Elbaz C, Antoniewski C, Huynh J-R. tRNA processing defects induce replication stress and Chk2-dependent disruption of piRNA transcription. EMBO J. 2015;34: 3009–3027. doi:10.15252/embj.201591006

2. Extract fastq files
3. for each file, select 8,000,000 (8 millions) of sequence reads and generate the following sample files:

ERR990557s.fastq

ERR990558s.fastq

ERR990559s.fastq

ERR990560s.fastq

4. Align these read datasets to the reference genome by any appropriate mean, and generate a sorted bam alignment file.
5. Count reads aligning to genome's genes by any appropriate mean
6. Perform a statistical differential expression analysis and report using any appropriate figure(s)/graph(s)
7. select a list of genes likely to be differentially expressed with a p-adj value < 0.01
8. Code a simple script that parse the table of differential expressions (from 6.) and return the genes with a p-adj value < 0.01 for rejection of H0 (non differential expression)

Reporting

Each analyst will report her/is analysis by any mean s/he feels appropriate (pdf, text, markedown, jpg, URL, etc.).

The only constraint is that analysis outputs will be deposited in a personal fork of this repository in a new directory named analysis.01, analysis.02, etc. (see analysis.00 for an example). Keep track of the analysis.xx directories already existing and chose another name for your directory.

Final submission of the results will be made through a pull request from the analyst to the original repo.

Please do not neglect the reporting and follow the requested process, it is a part of the analysis.