More than 20% molitems trashed

[jayypaul]

Hello,

For one of my timepoints, I received these 4 warnings lines that appeared as periodically after the sorting of the bam file (during the actual counting I believe). Could I get an explanation of what these warnings mean? I couldn't parse out the information in the source code. Please see below.

2018-11-05 12:43:15,574 - WARNING - More than 20% (26.2%) of molitems trashed, of those:
2018-11-05 12:43:15,574 - WARNING - A situation where many genes were compatible with the observation in 0.0 cases
2018-11-05 12:43:15,575 - WARNING - No gene is compatible with the observation in 25.1 cases
2018-11-05 12:43:15,575 - WARNING - Situation that were not described by the logic in the 1.1 of the caes

Furthermore, when each loom file was made, Velocyto would specify that a certain number of reads were skipped because no appropriate cell or umi barcode was found. To my understanding, cellranger gets rid of these reads prior. Is this common and would you be able to provide a reason as to why?

Thanks for your time.