I am trying to run some bam files though a pipeline that requires the bam files to contain the assignments of entire reads not read mates. I am using the Slide-seq2 data (from https://singlecell.broadinstitute.org/single_cell/study/SCP815/highly-sensitive-spatial-transcriptomics-at-near-cellular-resolution-with-slide-seqv2#study-summary ) which is not a single cell protocol and I am not sure what the bam files look like.
I would greatly appreciate some help to determine whether the bam files contain the assignments of the entire reads /entire alignment/ or read mates. And if they contain the read mates, how can I generate bam files containing the entire read alignments?
Thanks a lot!