KeyError: "tag 'CB' not present"

[kaplinserm]

Hi,

I have been following the dropest pipeline with my indrop v3 dataset and I want to use velocyto.

This is my method :

droptag -p 12 -s -c /home/user/dropEst/configs/indrop_v3.xml -t TCAGGATA -n data /Volumes/HD/source/cell_R2.fastq.gz /Volumes/HD/source/cell_R4.fastq.gz /Volumes/HD/source/cell_R1.fastq.gz /Volumes/HD/source/cell_R3.fastq.gz

tophat2 -p 12 --no-coverage-search -G /Volumes/HD/user/hg38.ncbiRefSeq.gtf -o /Volumes/HD/tophat/data/ /Volumes/HD/user/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index /Volumes/HD/droptag/data.1.fastq.gz,/Volumes/HD/droptag/data.2.fastq.gz,/Volumes/HD/droptag/data.3.fastq.gz,/Volumes/HD/droptag/data.4.fastq.gz,/Volumes/HD/droptag/data.5.fastq.gz,/Volumes/HD/droptag/data.6.fastq.gz,/Volumes/HD/droptag/data.7.fastq.gz,/Volumes/HD/droptag/data.8.fastq.gz,/Volumes/HD/droptag/data.9.fastq.gz,/Volumes/HD/droptag/data.10.fastq.gz

dropest -m -V -b -f -g /Volumes/HD/user/hg38.ncbiRefSeq.gtf -c /Volumes/HD/dropest/indrop_v3.xml -r /Volumes/HD/dropest/data.params.gz /Volumes/HD/dropest/accepted_hits.bam

sambamba sort -t 12 -p /Volumes/HD/sambamba/accepted_hits.tagged.bam

velocyto tools dropest-bc-correct /Volumes/HD/velocyto/accepted_hits.tagged.sorted.bam /Volumes/HD/velocyto/cell.counts.rds

I am receiving this error : KeyError: "tag 'CB' not present"

What is wrong with my method please ?

Thank you very much by advance.

[evanbiederstedt]

EDITED: We're working on compatibility with 10x and v3. Hopefully we'll have fixes soon.

[kaplinserm]

We're working on compatibility with 10x. Hopefully we'll have fixes soon.

Hello,

I am using indrop v3 and not 10x

Best regards