Tweet
In recent days, I am analyzing a whole human genome sequencing Illumina data. I used bowtie (-n -m 2) and bwa (default) respectively, and found the overlap of SNP calling was 60%. So, anybody met the same situation? and what was wrong with it?
-
-
They work in a different way... bowtie doesn't allow indels in alignment and it may be missing a lot of SNP -
are your quality values illuimna/Sanger? if it is illumina, bowtie can get illumina quality (with the option --solexa1.3-quals) and then the output is Sanger quality.
but in bwa, the quality of the output is like the input you give- without conversion. So make sure that after bowtie/bwa - you have the same quality format (which should be Sanger for Samtools and for many other applications).Comment
-
The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...02-24-2025, 06:31 AM
Comment