Can't select genome instead of transcriptome

[melispyilmaz]

Hi,
When I try to run MOP2 with "genome" as the reference type instead of "transcriptome" it doesn't create results. But it seems to be running (with the reference genome I provide) using "transcriptome" as the ref_type it seems to be working. The log file doesn't state any errors, in fact, it doesn't provide any lines after:

----------------------CHECK TOOLS -----------------------------
basecalling : guppy

demultiplexing will be skipped
mapping : minimap2
filtering : nanoq
counting : nanocount
discovery will be skipped

[- ] process > flow1:GUPPY_BASECALL:baseCall -
[- ] process > flow1:NANOQ_FILTER:filter -
[- ] process > preprocess_flow:MinIONQC -
[- ] process > preprocess_flow:MINIMAP2:map -
[- ] process > preprocess_flow:SAMTOOLS_CAT:catAln -
[- ] process > preprocess_flow:SAMTOOLS_SORT:sortAln -
[- ] process > preprocess_flow:SAMTOOLS_INDEX:indexBam -
[- ] process > preprocess_flow:checkRef -

[lucacozzuto]

Can you type the command line and attach the log file?

[rugilemat]

@melispyilmaz I think the issue is that you are using nanocount for counting which needs transcriptome reference. htseq works with genome.