search

10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
Other
342 stars 91 forks source link

running cellranger count for one sample on a common directory #118

Closed mmfalco closed 3 years ago

mmfalco commented 3 years ago

Hi, I've been trying to run cellranger count (v5.0.0) to get the counts for a sample I'm interested in. All the available fastq files from several samples are under the same directory and my sample of interest (included in this folder) has been sequenced in 2 lanes, but this is not supposed to be a problem according to your guidelines(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input#noproject). So for my sample of interest, I run the following command: cellranger count --id=SAMPLE1_SC --transcriptome=/shared/resources/references/cellranger_GRCh38d1vd1_mkref --fastqs=/shared/raw_data/fastq --sample=SAMPLE1_SC

And get this error: Some files in the fastq path /shared/raw_data/fastq are split by lane, while some are not. This is not supported. Caused by: Some files in the fastq path /shared/raw_data/fastq are split by lane, while some are not. This is not supported.

In /shared/raw_data/fastq along with other fastq files I have the following files for my sample of interest:

SAMPLE1_SC_S7_L001_I1_001.fastq.gz  SAMPLE1_SC_S7_L001_R2_001.fastq.gz  SAMPLE1_SC_S7_L002_R1_001.fastq.gz
SAMPLE1_SC_S7_L001_I2_001.fastq.gz  SAMPLE1_SC_S7_L002_I1_001.fastq.gz  SAMPLE1_SC_S7_L002_R2_001.fastq.gz
SAMPLE1_SC_S7_L001_R1_001.fastq.gz  SAMPLE1_SC_S7_L002_I2_001.fastq.gz

Moving all the files from the same sample to an individual folder seems to work but, is there any way to use this common folder to get the counts? I am especially concerned about this issue in the case I want to develop a pipeline to analyze all the samples. I don't see it very efficient if I must copy all the fastq files from a sample to individual folders.

mmfalco commented 3 years ago

After exchanging some emails with 10x helpdesk, we came to the conclusion that most probably is due to a conflict with some of the filenames which I could identify because I could not share the actual names due to privacy issues. A workaround that solved this is to create a new folder and create there symbolic links to the actual FASTQ files, instead of actually moving the files to individual folders. For example: ln -s SOMEPATIENTID_SC_S3_L002_R1_001.fastq.gz. newfolder/SOMEPATIENTID_SC_S3_L002_R1_001.fastq.gz