Demultiplex after clustering / genome alignment

[davidvilanova]

Hi.
I went through the latest isoseq pipeline (v4.1.1) to run an inoseq experiment.

I have started with a single bam files containing 3 samples did all the steps and I have run the isoseq clustering and genome alignment

I would like to create a count matrix for each sample.

I have tried

demux_isoseq_with_genome.py --mapped_fafq alignments2/aligned.sorted.fq --read_stat collapse2/isoform.read_stat.txt --classify_csv cluster2/merged_transcripts.cluster_report.csv --primer_names ../primers/barcodes.fa -o output

As far as i understand:

• aligned.sorted.fq is the alignmed sorted fastq file coming from the alignment to the reference genome (converted sorted bam fo fq)

• The isoform.read_stat.txt comes from Isoseq collapse

• the primer_names not sure which format is required. My samples are barcoded so i have a fasta file for each barcode used, but this is not working.

What´s wrong ? Am i missing something ?