cellranger count error: No input FASTQs were found for the requested parameters.
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3 months ago
tiancaigg ▴ 10

/mnt/Donghui_shared/Ann_SC_2020/X401SC21012937-Z01-F001/raw_data/JAL_1h » ls -a

     JAL_1h-AK3563_S2_L001_HG2VYCCX2_I1_001.fastq.gz  JAL_1h-AK3564_S3_L001_HG2VYCCX2_R2_001.fastq.gz
..                                               JAL_1h-AK3563_S2_L001_HG2VYCCX2_R1_001.fastq.gz  JAL_1h-AK3565_S4_L001_HG2VYCCX2_I1_001.fastq.gz
JAL_1h-AK3562_S1_L001_HG2VYCCX2_I1_001.fastq.gz  JAL_1h-AK3563_S2_L001_HG2VYCCX2_R2_001.fastq.gz  JAL_1h-AK3565_S4_L001_HG2VYCCX2_R1_001.fastq.gz
JAL_1h-AK3562_S1_L001_HG2VYCCX2_R1_001.fastq.gz  JAL_1h-AK3564_S3_L001_HG2VYCCX2_I1_001.fastq.gz  JAL_1h-AK3565_S4_L001_HG2VYCCX2_R2_001.fastq.gz
JAL_1h-AK3562_S1_L001_HG2VYCCX2_R2_001.fastq.gz  JAL_1h-AK3564_S3_L001_HG2VYCCX2_R1_001.fastq.gz

But running cellranger count always has error:

 /mnt/Donghui_shared/Ann_SC_2020/X401SC21012937-Z01-F001/raw_data/JAL_1h » cellranger count --id=JAL_1h-AK3562 --transcriptome=/mnt/chaelab/donghui/SC_Ann_JAL/Ath.Ensembl49.ref --fastqs=/mnt/temp/X401SC21012937-Z01-F001/raw_data/JAL_1h/ --sample=JAL_1h-AK3562
error: No input FASTQs were found for the requested parameters.

If your files came from bcl2fastq or mkfastq: - Make sure you are specifying the correct --sample(s), i.e. matching the sample sheet - Make sure your files follow the correct naming convention, e.g. SampleName_S1_L001_R1_001.fastq.gz (and the R2 version) - Make sure your --fastqs points to the correct location. - Make sure your --lanes, if any, are correctly specified.

Refer to the "Specifying Input FASTQs" page at https://support.10xgenomics.com/ for more details.

I tried a lot but it doesn't work. Can anybody suggest how to fix this?

scRNA cellranger • 297 views
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It doesn't look like you tried changing your names to match the correct naming convention.

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JAL_1h-AK3562_S1_L001_HG2VYCCX2_I1_001.fastq.gz

should be changed to

JAL_1h-AK3562_S1_L001_I1_001.fastq.gz

If you want to keep the FC serial HG2VYCCX2 in the names then add it before _S* in file names and then adjust your --sample= accordingly.

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oh it works. I didn't notice that what behind "S1" is also required by the pipeline's regex. Thanks

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Thanks. I rename the files and it works.

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