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Hello all,
I'm really a beginner in Bioinformatics. I start study about Bioinformatics, especially in NGS like 2-3 weeks ago. What I already learned is the basic concept of NGS and the data type that is produced by NGS machine. I also learned about analysis workflow of NGS data starting from the raw data to the end of analysis but only the global picture without getting into detail. So, I started to do my practical training with actual data I download from NGS SRA (it's a RRBS data). Here is what I've done:
1. Download the SRA
2. Use fastq-dump to convert SRA to fastq
3. Use FastQC for quality control
4. Use trim-galore for cut the adapter
5. Alignment to refrence genome
6. .....
So, for the first 4 step, I think it's easy to understand and the tools also really easy to use. Now, I'm stuck with alignment step. I check there are many tools and algorithm to do. I also found that method for alignment ordinary sequencing data and bisulfite sequencing data is different. I think I need to know and understand the basic concept of DNA alignment process, what is the algorithm, what is the popular tools. After all of that I can continue to understand about bisulfite sequencing. So, maybe all of you with many experience can share with me some knowledge about DNA alignment and the latest technology and development in DNA alignment step? If you have a list of papers to read I also accepted that I just confused with many algorithm, tools, and papers to read. I don't know where to start and what is the latest method. Thank you in advance.
*PS
List of paper that I plan to read:
A survey of sequence alignment algorithms for next-generation sequencing
A survey of tools for variant analysis of next-generation genome sequencing data
I also have several papers for each tools for aligning DNA sequence. I think I will prioritize to read those 2 because it's like a general comparison.
I'm really a beginner in Bioinformatics. I start study about Bioinformatics, especially in NGS like 2-3 weeks ago. What I already learned is the basic concept of NGS and the data type that is produced by NGS machine. I also learned about analysis workflow of NGS data starting from the raw data to the end of analysis but only the global picture without getting into detail. So, I started to do my practical training with actual data I download from NGS SRA (it's a RRBS data). Here is what I've done:
1. Download the SRA
2. Use fastq-dump to convert SRA to fastq
3. Use FastQC for quality control
4. Use trim-galore for cut the adapter
5. Alignment to refrence genome
6. .....
So, for the first 4 step, I think it's easy to understand and the tools also really easy to use. Now, I'm stuck with alignment step. I check there are many tools and algorithm to do. I also found that method for alignment ordinary sequencing data and bisulfite sequencing data is different. I think I need to know and understand the basic concept of DNA alignment process, what is the algorithm, what is the popular tools. After all of that I can continue to understand about bisulfite sequencing. So, maybe all of you with many experience can share with me some knowledge about DNA alignment and the latest technology and development in DNA alignment step? If you have a list of papers to read I also accepted that I just confused with many algorithm, tools, and papers to read. I don't know where to start and what is the latest method. Thank you in advance.
*PS
List of paper that I plan to read:
A survey of sequence alignment algorithms for next-generation sequencing
A survey of tools for variant analysis of next-generation genome sequencing data
I also have several papers for each tools for aligning DNA sequence. I think I will prioritize to read those 2 because it's like a general comparison.
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