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(1) Enhanced input data compatibility: The pipeline supports simultaneous processing of multiple sequencing lanes and additionally sequenced fastq files as input in a single analysis run, providing improved compatibility and batch processing capabilities.
(2) Consistent 1-based indexing: Both CB3 (cellular indexing barcode) and CB2 (sample indexing barcode) now utilize 1-based numbering systems, ensuring standardization across all barcode indexing schemes.
(3) Fixed intergenic quantification bug: Resolved the issue with zero intergenic read counts in gene quantification results, which was identified as a STAR aligner version-specific problem. Upgraded from STAR version 2.7.10b to 2.7.11a to address this quantification error.
python ${script_path}/CellCosmo_UHT.py \
--script_path ${script_path} \
--Rawdata_path ./0-data \
--SampleName 'test1 test2' \
--CB3_Num '1-20' \
--STARindex /path/GRCh38_index \
--TopCells 3000 \
--STARsoloThreads 2 \
--SplitcodeNum 10 \
--nFastqs 2 \
--soloFeatures 'GeneFull_Ex50pAS Velocyto' \
--outRaw True \
--Summary summary.txt \
--Mapping mapping.txt \
--LogFile log.txt \
--splitCB "[1,89,8] [2,90,8] [3,91,8] [4,92,8] [5,93,8] [6,94,8] [7,95,8] [8,96,8]" \
--splitSample "A B C D E F G H"