I ran kraken on my samples and generated results for the same. However, I am quite confused of which file, either kraken.result or kraken.report should be considered as final output.
Here is a sample report of my data (db used was minikrakendb):
78.58 632256 632256 U 0 unclassified 19.45 156475 3197 D 2 Bacteria 6.38 51349 586 D1 1783272 Terrabacteria group 5.73 46078 804 P 1239 Firmicutes
It seems that, 78% of my reads are unclassified.
Also, as per the report, does it mean that, in row #3, among all the reads in my raw fastq (input), only 51349 reads belonged to terrabacteria group? Or, does kraken performs a filtering step before classification, so that, if I had 100000 reads in my raw input fastq file, and kraken filtered them to (for instance) 80000, and among those 51,349 only mapped to terrabacteria?
One more final query is that, I have a list of TaxIDs and species names from the kraken report. Are there any R packages which can retrieve pathways of those taxIDs or species names?