What are the various procedures involved in DNA Mapping ?

Question

[plabanbiswas96]

Hello,

I am new to the field of BioInformatics, I have selected DNA Mapping using hadoop as my project and I will using java for this project (maven for build). I need to know what are the steps for DNA Mapping (like which file formats are required for input, how to map it to reference genome and what is the output file) and what are the available libraries for my project (I have come across samtools and hadoop-bam) .

I have come across htsjdk-SAM, FASTQ, BAM etc but can't figure out what to use as input for mapping and how to map it.

Thank You,

[IP]

I would begin reading this How to map billions of short reads onto genomes. And then I would google how to use a given aligner. I recommend you to use bwa-mem. Here is an overview of the commands bwa. The input to an aligner is a fastq file, and the output is sam/bam file.

[plabanbiswas96]

So, as far my understanding goes DNA sequence is present in FASTQ format, then it is mapped against a Reference genome which creates a SAM file and the SAM file has coordinates of mapped DNA. Right?

[IP]

exactly. The sam format has a lot of information about the alignment like mapping quality...

[plabanbiswas96]

Thanks for the information and swift reply :-)