I'm currently analyzing two samples of eosinophil cells isolated from mouse lung and the samples are of very different quality.
According to the Cell Ranger summary 56% of the reads can be mapped to the transcriptome in the first sample and only 32% in the second sample. Also the number of cells identified in Cell Ranger are very differnt (5000 for sample 1 and 600 for sample 2).

When I look at the raw data in FastQC I see that the second sample has a lot of poly-A sequences in the R2 read that obviously can't be mapped to the transcriptome.

Sample 1:
per base sequence content sample 1

Sample 2: per base sequence content sample 2

Also in many cases there is the following sequence in front of the poly-A:

To me it looks as if most of the reads do not contain an insert and are primer dimers. Is this connected to the lower cell count in the second sample?
Maybe some of you have already seen something like this and have a suggestion on how to avoid such a problem in the future.

Thanks a lot


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