Input data for IsoQuant for single cell pacbio

[leewqa]

Hi IsoQuant team,

I have a single cell Pacbio long read RNA data and would like to use IsoQuant for isoform quantification. I had previously ran the Iso-seq pipeline for pre-processing and had obtained deduplicated mapped bam file with poly-A tail trimmed. I am trying to understand what input file should be used for single cell IsoQuant - should it be unmapped deduplicated bam file with poly-A tail retained? And is there any documentation or recommendations for running single cell IsoQuant?

Thanks a lot for your help!

Best,
Audrey

[andrewprzh]

Dear @leewqa

The single-cell pipeline is not yet fully released. There is a forked version here: https://github.com/algbio/spl-IsoQuant
or you can try using IsoQuant from sc_3.9 branch.

IsoQuant will do everything by itself - barcode calling, PCR deduplication etc. So you can provide raw CCS reads in umapped BAM or FASTQ, preferably with polyA tails.

As there is no full manual yet, feel free to ask questions. I hope it will be release soon.

Best
Andrey