RNAseq-analysis

The repository has all the scripts used for the DE Analysis.

list_samples_names.txt

List of the samples names

0_fastqc.sh

Run FasQC app to check the quality of the data.

1_run_trimmomatic.sh

Run trimmoatic to remove the adaptors of the data.

2_run_tophat_TRIM_ncbi.sh

Mapping the reads to the genome (before this step you have should created the genome index).

3_htseqcount.sh

Perform the read-counts.

4_tablecounts.sh and Extract_tablecounts_from_counts.pl

It uses the file "Extract_tablecounts_from_counts.pl" to extract the counts for each gene.

DE_analysis.R

R Script with all the code to process the data and perform the DE Analysis.

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Author: Cècile Pereira - cecile.pereira.bibs(at)gmail.com