/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?
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It doesn't look like you tried changing your names to match the correct naming convention.
should be changed to
If you want to keep the FC serial
HG2VYCCX2in the names then add it before_S*in file names and then adjust your--sample=accordingly.oh it works. I didn't notice that what behind "S1" is also required by the pipeline's regex. Thanks
Thanks. I rename the files and it works.