methodology

RNA seq data analysis
1.Raw Dataset First of all,we retrieve the genomic data set from NCBI SRA database (http://www.ncbi.nlm.nih.gov/sra/SRX1769933%5Baccn%5D).
Then covert this dataset to FASTQ format using sra toolkit. 
2.Quality Check Data quality assessment (QA) and exploration are essential steps of any data analysis.
These steps should typically be performed very early in the analysis of a new data set, preceding or in parallel to the normalization step and differential expression testing. 
3.Alignment Raw data of colorectal cancer used in Bowtie software used for alignment is in FASTQ format.
FASTQ files are ASCII text files that encode both nucleotide calls as well as 'quality information', which provides information about the confidence of each nucleotide. 
FASTQ format uses 4 lines for each read produced by the sequencer. 
Fastq files are normally given the file extension ".fq" or ".fastq". 
Alignment, also called mapping, of reads is an essential step in re​ sequencing.
Having sequenced an organism of a species before, and having constructed a reference sequence, re​ sequencing more organisms of the same species allows us to see the genetic differences to the reference sequence, and, by extension, to each other. 
Alignments of data from these re​ sequenced organisms is a relatively simple method of detecting variation in samples
 4.Differential expression analysis Differential expression (DE) analysis using RNA​ seq is commonly employed to interrogate changes between different experimental conditions.
 5.Pathway analysis