bpuzek

Hi @andrewprzh, thank you for the great software! I might be experiencing the same issue as @HabiBBBaghirov, with read groups being recognised but not used for generating a per-group matrix....

Dear Andrey, here are the file list and log files. [isoquant.log](https://github.com/ablab/IsoQuant/files/15119605/isoquant.log) [alignment.log](https://github.com/ablab/IsoQuant/files/15119607/alignment.log) [filelist.txt](https://github.com/ablab/IsoQuant/files/15119608/filelist.txt) Many thanks in advance, Barbara

Dear @andrewprzh, here the first few lines of the file. Only one column of counts, instead of one column per cell as expected: ``` #feature_id NA ENST00000003583.12 4.67 ENST00000003912.7 0.00...

Dear @andrewprzh any news on this? Thanks, Barbara

Dear @andrewprzh, Preparing the files to send I noticed that read IDs in read_group file were not matching those in fastq files and thus all reads were assigned to the...

Dear @andrewprzh, thank you so much for all the good work on recent isoquant developments! Similar to Mangosteen24 we've observed multiple confusing scenarios when exploring SAMPLE_ID.transcript_counts.tsv and SAMPLE_ID.transcript_model_counts.tsv entries. Some...