fail in docker: Total 0 white-listed Barcodes

[LinAU]

Thanks for your work. Everything works well with the demo testing data. However, when I have tested scRNAseq data from 10xgenomics 3' v2. Although the first part runs well. all reads were filtered out due to no white listed BC as lalevin.log file below:

[2024-03-18 20:40:50.427] [alevinLog] [info] Found 70629 transcripts(+0 decoys, +0 short and +0 duplicate names in the index) [2024-03-18 20:40:50.466] [alevinLog] [info] Filled with 70629 txp to gene entries [2024-03-18 20:40:50.472] [alevinLog] [info] Found all transcripts to gene mappings [2024-03-18 20:40:50.479] [alevinLog] [info] Processing barcodes files (if Present)

[2024-03-18 20:54:52.178] [alevinLog] [info] Done barcode density calculation. [2024-03-18 20:54:52.178] [alevinLog] [info] # Barcodes Used: [32m316403175[0m / [31m316403175[0m. [2024-03-18 20:54:52.178] [alevinLog] [info] Done importing white-list Barcodes [2024-03-18 20:54:52.178] [alevinLog] [warning] Skipping 200 Barcodes as no read was mapped [2024-03-18 20:54:52.178] [alevinLog] [info] Total 0 white-listed Barcodes [2024-03-18 20:54:52.178] [alevinLog] [info] Sorting and dumping raw barcodes [2024-03-18 20:54:58.507] [alevinLog] [warning] Total 100% reads will be thrown away because of noisy Cellular barcodes. [2024-03-18 20:54:58.507] [alevinLog] [info] Done populating Z matrix [2024-03-18 20:54:58.507] [alevinLog] [warning] 0 Whitelisted Barcodes with 0 frequency [2024-03-18 20:54:58.507] [alevinLog] [info] Total 0 CB got sequence corrected [2024-03-18 20:54:58.507] [alevinLog] [info] Done indexing Barcodes [2024-03-18 20:54:58.507] [alevinLog] [info] Total Unique barcodes found: 892257 [2024-03-18 20:54:58.507] [alevinLog] [info] Used Barcodes except Whitelist: 0 I used the whitelist file from cellranger, and here it is my docker parameters: #!/bin/bash

main parameters

INPUT="/mnt/d/data_analysis/Analysis_2023_NAFLD_sc/9.isoform.analysis_v2/5.NAFLD.docker/1.fq/GSM4041150" OUTPUT="/mnt/d/data_analysis/Analysis_2023_NAFLD_sc/9.isoform.analysis_v2/4.test.docker/ScasaOut_v10" ref="/mnt/d/data_analysis/Analysis_2023_NAFLD_sc/9.isoform.analysis_v2/4.test.docker/refMrna.fa.gz" index="YES" #when index="YES", scasa will index the reference fasta file and write in index_dir. This index_dir cam be reused for other run #index_dir="/path/to/PreBuilt_REF_INDEX" #when index="NO", scasa will use directly the reference indexing in index_dir nthreads=12 tech="10xv2" whitelist="/mnt/d/data_analysis/Analysis_2023_NAFLD_sc/9.isoform.analysis_v2/4.test.docker/Test_Dataset/737K-august-2016.txt" cellthreshold="none" project="My_Project"

other parameters

samplesheet="NULL" mapper="salmon_alevin" xmatrix="alevin" postalign_dir="" createxmatrix="NO"

May I ask for your help? Thanks a lot! KR Lin