I have just begun working through the Moving Pictures tutorial and after running DADA2 I want to know how many sequences were input, filtered, denoised and chimeric for each sample. I used the “verbose” option which output some information to the screen, however only for the following samples?..
Do you know why there is only info for a few samples? Is there a log file which is created which tracks samples through each step?
Also after carrying out the DADA2 denoising, I am obviously interested to look at the ASV table directly and quickly see how many features per sample and the abundance of each feature in each sample. There seems to be no way to simply open this table?? I have generated the summary files however the information they provide is limited. Is the only way to view this table to first export to biom then convert to text?
It looks like we're using R's head function to look at only the first few samples. There isn't a log yet, but we have an issue tentatively planned for this upcoming release to turn that information into an artifact (viewable as metadata) letting you track this for each sample (and even use it downstream if you needed).
Typically there is so much information, that looking at it that way isn't the most informative since it contains hundreds of thousands (to millions) of values. If you want to look at it in Excel or similar, then you will need to export and use biom to convert like you described. We do have plans to make exporting to other formats simpler (skipping the biom step), but that's probably not going to make it into this release.
So it is correct that currently there is no way of determining how many reads were removed due to low quality, phiX and chimericity during the DADA2 denoising step?