I am trying to use CellRanger 'count' function on the 10x single-cell data deposited here (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8077/). I tried it two ways:
1) While in the directory where the fastq.gz files are:
cellranger count \ --id=Kalucka_endo \ --fastqs=<path> \ --transcriptome=[path]/refdata-cellranger-mm10-3.0.0
2) with the sample 'prefix':
cellranger count \ --id=Kalucka_endo \ --sample=<sample_ID_prefix> \ --fastqs=<path> \ --transcriptome=<path>/refdata-cellranger-mm10-3.0.0
They state that they used 10x for sequencing but it isn't clear to me that their samples were named using bcl2fastq or demux. An example of one of their samples is 180908_I127_FCHWNVWBBXX_L1_CDKPEI180829002-ATTCTAAG_S1_L001_R2_001.fastq.gz and 180908_I127_FCHWNVWBBXX_L5_CDKPEI180829002-ATTCTAAG_S1_L001_R2_001.fastq.gz.
I tried using 10x tutorial data here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ct#explorecount
and was successfully able to get it running using the command line from 1) while in the directory with the fastq.gz files.
When I try either of these two ways of running it with this data, I getting this traceback:
`cellranger count (3.1.0) Copyright (c) 2019 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Invalid path/prefix combination:
, None 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. Refer to the "Specifying Input FASTQs" page at https://support.10xgenomics.com/ for more details.`
I tried changing the name to reflect a name more consistent with bcl2fastq naming convention i.e.
<sample name> _ <barcode sequence>_L<lane>_R<read number>_<setnumber>.fastq.gz
for example I made 180908_I127_FCHWNVWBBXX_L1_CDKPEI180829002-ATTCTAAG_S1_L001_R2_001.fastq.gz to be brain1_ATTCTAAG_L001_R2_001.fastq.gz 180908_I127_FCHWNVWBBXX_L5_CDKPEI180829002-ATTCTAAG_S1_L001_R2_001.fastq.gz. to be brain2_ATTCTAAG_L001_R2_001.fastq.gz
With these changes, I am still getting the aforementioned error.
The only other forum question that I was able to find was this one: cellranger count help and I don't believe I am having the same issue as even using no sample name and using a '.' for the --fastqs
Any thoughts or suggestions are greatly appreciated!