Missing genes in count matrix
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I have some single-cell RNA-seq data I am trying to process with dropEst. Everything seems to be working really nicely except that the generated matrices do not have any counts for the adult beta- or alpha-globin genes (which are important because this is an erythroid dataset). I do have counts for the embryonic globin genes. I have checked my bam files and there are many reads covering these genes, I have also checked that at least some of these reads come from cell barcodes that make it into the final matrix file.
I had thought that this might be to do with multimapping as the adult globin genes are both duplicated whilst the embryonic globin genes are not, so all the reads mapping to these genes have NH:i:2 in the optional sam fields. I therefore edited the bam files to keep only primary alignments and rewrite "NH:i:2" to "NH:i:1" so that dropEst does not know they are multimapped. However this doesn't fix the problem, and I still get no output for any of these genes after running dropEst. Do you have any suggestions for how I might be able to troubleshoot this?
Thanks for the help!
Rob