no matrix.mtx.gz in cellranger output

Question

[yueli7]

Hello,

I followed link to run cellranger count

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ct

It said in the folder filtered_feature_bc_matrixshould have three files, I have barcodes.tsv.gz, features.tsv.gz, but I do not have matrix.mtx.gz.

Thanks in advance for any great help!

Best,

Yue

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

yli1@rsc01:~/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin$ ./cellranger count --id=run_count_1kpbmcs --fastqs=pbmc_1k_v3_fastqs --sample=pbmc_1k_v3 --transcriptome=refdata-cellranger-GRCh38-3.0.0
/home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin
cellranger count (3.1.0)

-------------------------------------------------------------------------------

Martian Runtime - '3.1.0-v3.2.3'
2020-02-15 19:47:02 [runtime] Reattaching in local mode.
Serving UI at http://rsch-rnk-srv01:45321?auth=pCJTYv51zW6kiE4XzBWImlUAx8UyxO9UJTtqbmEg1AA


Outputs:
- Run summary HTML:                         /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/chnk0-u7461478aec/files/web_summary.html
- Run summary CSV:                          /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/chnk0-u7461478aec/files/metrics_summary_csv.csv
- BAM:                                      /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SORT_BY_POS/fork0/join-u74614786bb/files/output.bam
- BAM index:                                /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SORT_BY_POS/fork0/join-u74614786bb/files/output.bam.bai
- Filtered feature-barcode matrices MEX:    /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u7461478915/files/filtered_matrices_mex
- Filtered feature-barcode matrices HDF5:   /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u7461478915/files/filtered_matrices_h5.h5
- Unfiltered feature-barcode matrices MEX:  /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-u74614786bb/files/matrices_mex
- Unfiltered feature-barcode matrices HDF5: /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-u74614786bb/files/matrices_h5.h5
- Secondary analysis output CSV:            /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u7461478a15/files/analysis_csv
- Per-molecule read information:            /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/REPORT_MOLECULES/fork0/join-u74614789bd/files/output.h5
- CRISPR-specific analysis:                 null
- Loupe Cell Browser file:                  /home/yli1/opt01/cellranger-3.1.0/cellranger-cs/3.1.0/bin/run_count_1kpbmcs/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/join-u7461478afa/files/output_for_cloupe.cloupe
- Feature Reference:                        null

Waiting 6 seconds for UI to do final refresh.
Pipestance completed successfully!

2020-02-15 19:47:08 Shutting down.
Saving pipestance info to "run_count_1kpbmcs/run_count_1kpbmcs.mri.tgz"

Answer 1

[yueli7]

I ran it again, and I found the matrix.mtx.gz is in the folder run_count_1kpbmcs/outs/filtered_feature_bc_matrix.

Last time, I unzip the file of run_count_1kpbmcs.mri.tgz.

So I can not found the file in run_count_1kpbmcs.mri.tgz.