My question is about single-cell rnaseq, but I believe people with experience with bulk RNA-seq might also be able to answer this.
I aligned a few single cell datasets with cellranger, but when I checked the results, it seems that although most reads aligned to to the genome (only half with high confidence), only 40% of the reads aligned with the transcriptome. Here is an example of one of the outputs:
Reads Mapped to Genome 96.6%
Reads Mapped Confidently to Genome 54.6%
Reads Mapped Confidently to Intergenic Regions 8.5%
Reads Mapped Confidently to Intronic Regions 0.2%
Reads Mapped Confidently to Exonic Regions 46.0%
Reads Mapped Confidently to Transcriptome 45.3%
Reads Mapped Antisense to Gene 0.4%
I am not sure what to think about this. Could this be a sign of low integrity of the reads? My hypothesis is that this if there is degradation in the sample, it could have not aligned as a trasncript, but it shouldn't have any problem aligning with the genome. Another hypothesis is that the sample was contaminated with genomic DNA. I am, however, not even sure if these results are normal.