I am analyzing scRNA data from Smart2-seq . I did the mapping by using Hisat2 .Some of the cells has reaaly low mapping rate (8%) us expected. I am wondering do I need to exclude these cells before the following steps ( filtering with samotools, featureCounts) or they can be excluded later in Seurat? If I need to exclude them prio in further analysis I should use a specific tool ?
Thanks in advance, A.