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alexdobin / STAR

RNA-seq aligner
MIT License
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STARsolo on scRNAseq #1793

Open ahlem1962 opened 1 year ago

ahlem1962 commented 1 year ago

hello Alex, I want to thank you first for your help. I'm performing STARsolo on pbmc fastq files and I'm using the reference genome from 10*genomics but I have this issu that I can't understand (the reference genome is indexed)

STAR version: 2.7.10b compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Mar 13 14:42:48 ..... started STAR run Mar 13 14:42:48 ..... loading genome EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.10b SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a Mar 13 14:42:48 ...... FATAL ERROR, exiting

this is the command line that I'm using:

/opt/conda/envs/scRNA_seq/bin/STAR --genomeDir /lab/user/bricks/reference/refdata-gex-GRCh38-2020-A/star --readFilesIn /lab/user/bricks/input/test_input/pbmc_1k_v3_fastqs/pbmc_1k_v3_S1_L001_R2_001.fastq.gz,/lab/user/bricks/input/test_input/pbmc_1k_v3_fastqs/pbmc_1k_v3_S1_L002_R2_001.fastq.gz /lab/user/bricks/input/test_input/pbmc_1k_v3_fastqs/pbmc_1k_v3_S1_L001_R1_001.fastq.gz,/lab/user/bricks/input/test_input/pbmc_1k_v3_fastqs/pbmc_1k_v3_S1_L002_R1_001.fastq.gz --soloType CB_UMI_Simple --soloCBwhitelist /lab/user/bricks/cellranger-7.1.0/lib/python/cellranger/barcodes/737K-arc-v1.txt --soloUMIlen 12 --soloCBlen 16 --soloUMIstart 17 --soloCBstart 1 --soloBarcodeReadLength 0 --clipAdapterType CellRanger4 --outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --outSAMtype BAM Unsorted --runThreadN 8 --outFileNamePrefix test --soloCellFilter EmptyDrops_CR --soloFeatures GeneFull

alexdobin commented 1 year ago

Hi @ahlem1962

the STAR index in refdata-gex-GRCh38-2020-A was generated by an old version of STAR and is incompatible with the new STAR version you are using. You would need to regenerate the genome index using the refdata-gex-GRCh38-2020-A/fasta/genome.fa and refdata-gex-GRCh38-2020-A/genes/genes.gtf files.