How to generate bam files containing the entire read alignments?

Question

[Arman]

Hello!

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!

[Carlo Yague]

It could have misunderstood your question, but if you really just want to see the number of reads mapped with their mates and the number of singletons, you can simply use samtools flagstat.