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biocorecrg / MOP2

Master of Pores 2
https://biocorecrg.github.io/MOP2/docs/
MIT License
23 stars 7 forks source link

Can't select genome instead of transcriptome #47

Open melispyilmaz opened 1 year ago

melispyilmaz commented 1 year ago

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 commented 1 year ago

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

rugilemat commented 1 year ago

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