I am preprocessing a set of scTHSSeq reads in which each read sequence identifier has been replaced with the cell barcode, e.g.:
@CGAGGCTG_TATCCTCT_AGTCCA ... ... ... @CGAGGCTG_TATCCTCT_GGTACG ...
The read sequence identifier has been replaced with the cell barcode to be able to demultiplex alignments after bwa into a different bamfile for each cell.
I ran the alignment using bwa mem and I received no errors. However I would like to know if there are caveats or reasons why this approach may lead to misleading results.
I will then proceed to remove PCR duplicates with
samtools rmdup executed in each cell's bamfile and then I'd run peak calling using spp.