Adding my report for the RNAseq analysis

README.md

@@ -1,48 +1,6 @@
-# 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](http://www.ebi.ac.uk/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](https://help.github.com/articles/fork-a-repo/) 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](https://help.github.com/articles/creating-a-pull-request/) from the analyst to the [original repo](https://github.com/drosofff/RNAseq.git).
-
-Please do not neglect the reporting and follow the requested process, it is a part of the analysis.
+# analysis.01
+
+## RNA-seq analysis
+
+You can find my report in the html document (rna_seq) in the same directory.  
+Best regards, L. Bellenger