Single cell data one library with different conditions

[vasikara17]

Hello, first of all thanks for this really useful tool! I have one BAM file with single nuclei data from 8 conditions. I run the isoquant like this: isoquant.py --reference /path/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz
--genedb path/Mus_musculus.GRCm39.112.gtf.gz --complete_genedb
--bam path/lib2.aligned.sorted.bam
--data_type 'nanopore'
--report_novel_unspliced true
-o path/isoquant_results
--sqanti_output Can I split the results based on condition and barcode or should I split the bam files first?

Thank you in advance, VK

[andrewprzh]

@vasikara17

Thanks for the feedback!

Could you please clarify, would you like to have a separate output for each condition, or an expression table with barcodes and conditions? How are you barcodes and conditions are stored?

Best Andrey

[andrewprzh]

Okay, following your post in https://github.com/ablab/IsoQuant/issues/211

So far IsoQuant supports only one way of grouping reads via --read_group, so either by condition or by barcode. This can be done using a separate table, i.e. read-barcode table, or BAM file tags. If you'd like to group by different criteria, unfortunately you have to run IsoQuant twice. I am planning to implement multiple read grouping in the future.

Best Andrey