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Hello Jagbir,
what have you tried so far to find out? You tagged this post with
aligment. So the first step seems to be known to you. What comes next is variant calling. A good starting point to get in touch with this kind of analysis are the GATK best practices guides.fin swimmer
Hi thanks for the reply I have tried aligning both the sequences using blast.
Basically I want to find out the mode of action of the novel compounds. I have generated the mutants of mycobacterium using high concentrations of these compounds and got the data for whole genome sequencing. I would like to compare this data with that of the wild type and see if there are any point mutations or SNPs. If they are any mutations, on what gene or genes they are associated with.
Thanks
Hello,
could you please elaborate a little bit more on what kind of data do you have? fastq from a sequencing project? fasta of the organism you like to compare? Anything other than that?
fin swimmer
Hi I do have the whole genome sequence data for both the organisms in fasta format also trimmed reads in fastq format
Kin Regards
BLAST is not suitable for this. This is not what #finswimmer meant by "alignment". BLAST simply takes a short query sequence and aligns it to a database to look for similar sequences to identify the origin of the query sequence. But you are looking at an entire genome.
What you need is an "aligner" that will take the entire fastq file/files and align them to a reference genome. There are many aligners out there including HISAT2 or STAR.
However, #finswimmer has already directed you to the best place to start your learning. The GATK pipeline is what you will most likely end up using to identify and analyize the SNPs, so go read what they say you should do in preparation.