ssmax1

Thanks for the quick reply, here is the head of the bam file - AGAGTCTACTAT_CACATGGC#ST-E00522:327:HK77CCCXY:3:1101:24312:4016 16 chr6 72385233 255 12S138M * 0 0 TTTTTTTTTTTTGATACCAAGAGGTCTTTATTGCCCACCAGCCACCAACAGTTTCCCAGCCACAGACAGGGTCCTCTGGGTCTCTGTAACCCACTCTCAGGACCATGAGATGCAGCTACAGTCCAGCTGTCTCCTCCCAGGGGATCAAGG JFJFJJFJJJFAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ

Hi Shian, I tried the ensembl GFF3 annotation which works, but have noticed that some exons seem to be excluded leaving many barcode matched and aligned but unassigned reads. I...

Thanks for the advice! I have since narrowed the problem down and managed to obtain counts for the exon of interest. As there are reads that aligned but not assigned...

Sorry, I was mistaken before, the reads that should appear in the exon are still not counted downstream. The summary from sc_exon_mapping indicates "unique map to exon" for these reads...

After further examination... If I remove all annotation from the Ensembl file "Mus_musculus.GRCm38.91.gff3" except for lines matching ENSMUSG00000037111 / Setd7 exons and linked parents - mRNA/ gene lines, the reads...

Hi Shian, Thank you, yes that is correct. I haven't pinned down which overlap was causing the problem, but excluding everything but the exon of interest did allow the reads...

Thanks for looking into this and for the suggestions @Shians & @LuyiTian. I am currently re-aligning my data, but will isolate the reads and try the C++ version once complete....