NCBI GEO is a repository of various gene expression profiling datasets.
If I would like make a comparative study and look for commonality between different datasets related to same class (disease type/drug type/sample used) what are the methods that are employed ?
Dear Goutham,
you can use SAM tool for comparative gene expression profiling. plz visit
http://statweb.stanford.edu/~tibs/SAM/
Use SAM tools to convert .sra file to .Fastq file. Check the quality of the data using FastQC. Trim adapter sequences and bad quality data using cutadapt. Download genome sequence in .fastq and .gff format and index them using bowtie2. Align RNASeq reads to the genome using bowtie2. Rest of the process you could find online.
Thank u every one I will look into individual tools and check the feasibility.
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