airichli

Hi, could ChromVAR be applied to two ATAC-seq sample from two plant tissues (like leaf and flower, not single cells)? If it could, is there any parameters that I should...

Inconsistency among *read_assignments.tsv, *.transcript_counts.tsv, and *.gene_counts.tsv

3

Hi, Thanks for developing this nice tool. I met one issue that the count is inconsistent among files as list in the title. My command line is: ./IsoQuant-3.5.0/isoquant.py -d nanopore...

Uniquely assigned reads seem non-unique

2

Hi, The *transcript_counts.tsv file seems to count non-unique reads as unique reads (I use the parameter --transcript_quantification unique_only --gene_quantification unique_only, so only unique reads would be considered). Here I show...

Model for ONT R10 data

2

Hi, Thanks for developing this nice tool. Currently, there is clair3 model for r1041_e82_400bps_hac_v5.0.0, is it OK to use this model for reads called from the latest dorado model [email protected]?...