StarSolo with parameters for matching Cell Rager 7.0.x generates an empty mtx file.

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akhst7

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Jan 28, 2023, 3:39:08 PM1/28/23
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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.  
 
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