Hi. I need help with SAM files. I have a SAM file but i dont have idea how to view the result to finds snp, coverage, etc. is there any program to view and interpret easier? thanks
what is the purpose of your analysis? SAM files store information about sequence alignment against a reference, but it doesn’t include explicit information about SNPs or coverage.
Hi Gallardo. Thanks for the answer. I have phaseolus vulgaris genome with the genes and the phaseolus lunatus only with the raw sequence and I downloaded the reads. I want to see if some genes of vulgaris are in lunatus (like nfr1, nfr5) and be able to make the annotation. The propouse is discover variation, snps. Sorry if i dont be clear I m new in bioinformatics.
in that case, I suggest you have a look at these two trainings:
however, I found that the genome of P. lunatus have been annotated already: annotation. Perhaps it can be useful for you.
Let me know if you have any additional questions as you begin the analysis.