I am very new to this gene expression analysis, i wanted to download NSG database from TCGA and other resources, and wanted to download only particular expression pattern for cancer subtype.Say in database you have expression data for breast cancer, that may contain diss subtypes. so i have pick specific subtypes and analyse,.And easier pipeline data analysis software also be suggested.
what are different ways i can represent the data also mentioned.thanks
Dear Suresh Kumar,
The NGS is a widely used nucleotide sequencing method, and the NGS data includes: 1) RNA-seq, 2) Chip-seq, 3) 3C related data (like Hi-C), 4) ribo-seq and so on. Each one could be viewed as a snapshot of a certain biological process. RNA-seq data represent the transcription. Hi-C data represent the chromatin interaction.
The general NGS data analysis procedure includes:
After these steps, you should keep data processing, and use specific pipeline for specific NGS data. For example, RNA-seq data processing should be followed by assembly using tophat. Assembly also need genome annotation files (file type ".GFF", or ".GTF").
Say you want to find transcription pattern in cancer sample, you may use some statistic methods in R. These methods include clustering, PCA, and so on.
Use the same data, different researchers can perform different analyzing procedures, and find different stories. There is a long way to master the data mining skills, and hope you can see more tutorials from google.
Best wishes,
Luezhen
Dear Suresh Kumar,
The NGS is a widely used nucleotide sequencing method, and the NGS data includes: 1) RNA-seq, 2) Chip-seq, 3) 3C related data (like Hi-C), 4) ribo-seq and so on. Each one could be viewed as a snapshot of a certain biological process. RNA-seq data represent the transcription. Hi-C data represent the chromatin interaction.
The general NGS data analysis procedure includes:
After these steps, you should keep data processing, and use specific pipeline for specific NGS data. For example, RNA-seq data processing should be followed by assembly using tophat. Assembly also need genome annotation files (file type ".GFF", or ".GTF").
Say you want to find transcription pattern in cancer sample, you may use some statistic methods in R. These methods include clustering, PCA, and so on.
Use the same data, different researchers can perform different analyzing procedures, and find different stories. There is a long way to master the data mining skills, and hope you can see more tutorials from google.
Best wishes,
Luezhen
Thanks Luezhen Yuan. I am beginner, trying to learn myself. thanks a lot
suresh
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