Hi, I was trying to use kallistobustools to preprocess a CEL-seq2 dataset with the pipeline provided by https://www.kallistobus.tools/getting_started.
My code is
kallisto bus -i $work_p/homo_ercc.idx -o bus_output/ -x CELSeq2 -t 4 $seq_p/SC1_S1_R1.fastq.gz $seq_p/SC1_S1_R2.fastq.gz
However, when it comes to
$bustools correct -w $data_p/barcode_annotation -p output.bus | $bustools sort -T tmp/ -t 4 -p - | $bustools count -o genecount/genes -g ../transcripts_to_genes.txt -e matrix.ec -t transcripts.txt --genecounts -
an error like this would come up. Error: barcode length and whitelist length differ, barcodes = 6, whitelist = 8 .check that your whitelist matches the technology used.
I am quite sure UMI length is 6, and cell barcode length is 8. Could you please help me find out what is the problem?
Hi, I was trying to use kallistobustools to preprocess a CEL-seq2 dataset with the pipeline provided by https://www.kallistobus.tools/getting_started. My code is
kallisto bus -i $work_p/homo_ercc.idx -o bus_output/ -x CELSeq2 -t 4 $seq_p/SC1_S1_R1.fastq.gz $seq_p/SC1_S1_R2.fastq.gzHowever, when it comes to$bustools correct -w $data_p/barcode_annotation -p output.bus | $bustools sort -T tmp/ -t 4 -p - | $bustools count -o genecount/genes -g ../transcripts_to_genes.txt -e matrix.ec -t transcripts.txt --genecounts -an error like this would come up. Error: barcode length and whitelist length differ, barcodes = 6, whitelist = 8 .check that your whitelist matches the technology used. I am quite sure UMI length is 6, and cell barcode length is 8. Could you please help me find out what is the problem?