npsonis
npsonis
Hi, still an issue today
-n 5 means that you will be able to map 95% of your reads successfully, assuming a 2% error rate. -n 6 means that you will be able to map...
Not so different compared to the rest... In fact, larger files worked without an issue...
Hi, I did not... This was in a prescreening run so I did not invest my time to solve it. When I run the same sample (but deep sequencing) I...
You can use the --omit-from command of snakemake and exclude the bowtie2 step.
Hi Nikolay, there is no KRAKENUNIQ_ABUNDANCE_MATRIX directory I am afraid.
In the krakenuniq.output.filtered the taxName field is empty in all species % reads taxReads kmers dup cov taxID rank taxName 3.563 914033 415742.0 14176.0 1720.0 0.0001958 63459.0 species 0.6799 174442...
So I did as you proposed. krakenuniq.output: % reads taxReads kmers dup cov taxID rank taxName 82.17 21081547 21081547 183323763 7.74 0.4916 0 no rank unclassified 17.83 4574147 6866 2028404...
I have used less strict filtering (50 and 250), but there are cases that exceed 200 and 1000. The problem is that with your solution there are two tabs between...
Well it could be not related to dos2unix as in another server that I am working (again with mobaexterm) I do not have this issue, albeit in that case I...