HI,
I've been trying yo run STARSolo, matching Cell Rager 7.0.x results as follows;
#!/bin/bash
index=/Volumes/Bioinformatics/star_genome_index/index_human
STAR --genomeDir $index \
--readFilesCommand gunzip -c \
--readFilesManifest /Volumes/Bioinformatics/manifest.txt \
--soloCBwhitelist /Volumes/Bioinformatics/star_genome_index/3M-february-2018.txt \
--soloType CB_UMI_Simple \
--soloCBstart 1 \
--soloCBlen 16 \
--soloUMIstart 17 \
--soloUMIlen 12 \
--clipAdapterType CellRanger4 \
--soloMultiMappers EM \
--soloFeatures Gene GeneFull SJ Velocyto \
--outFilterScoreMin 30 \
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
--soloUMIfiltering MultiGeneUMI_CR \
--soloUMIdedup 1MM_CR \
--outFileNamePrefix Solo_10X_5k_PBMC \
--outSAMtype BAM SortedByCoordinate \
--outSAMattributes CR UR CY UY CB UB
I generated a human STAR index based on a refdata-cellranger-GRCh38-3.0.0/genes/genes.gtf and refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa and 10X 5K PBMC as input fastq files.
The script above run fine except it generated empty outputs as follows;
Solo_10X_5k_PBMCLog.final.out
Started job on | Jan 28 11:03:24
Started mapping on | Jan 28 11:03:47
Finished on | Jan 28 11:06:13
Mapping speed, Million of reads per hour | 0.00
Number of input reads | 0
Average input read length | 0
UNIQUE READS:
Uniquely mapped reads number | 0
Uniquely mapped reads % | 0.00%
Average mapped length | 0.00
Number of splices: Total | 0
Number of splices: Annotated (sjdb) | 0
Number of splices: GT/AG | 0
Number of splices: GC/AG | 0
Number of splices: AT/AC | 0
Number of splices: Non-canonical | 0
Mismatch rate per base, % | nan%
Deletion rate per base | 0.00%
Deletion average length | 0.00
Insertion rate per base | 0.00%
Insertion average length | 0.00
MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 0
% of reads mapped to multiple loci | 0.00%
Number of reads mapped to too many loci | 0
% of reads mapped to too many loci | 0.00%
UNMAPPED READS:
Number of reads unmapped: too many mismatches | 0
% of reads unmapped: too many mismatches | 0.00%
Number of reads unmapped: too short | 0
% of reads unmapped: too short | 0.00%
Number of reads unmapped: other | 0
% of reads unmapped: other | 0.00%
CHIMERIC READS:
Number of chimeric reads | 0
% of chimeric reads | 0.00%
Matrix in Gene and Velocity has one entry;
%%MatrixMarket matrix coordinate integer general
%
36601 6794880 0
A barcode.tsv had 6794880 entries ;
wc -l barcodes.tsv
6794880 barcodes.tsv
I am getting stuck in solving this issue, and any help will be appreciated.