I am trying to run scRNA velocity with velocyto. A preliminary step is to run cellranger on fastq files but I have an issue with my chosen dataset
Here is what I did:
- Downloaded each SRR from GSE104323 using a loop with
fastq-dump --split-files --origfmt --gzip SRR6084134
- This only yielded one SRR file instead of 3 expected files (R1,R2,I1)
- I renamed my fastqs to:
SRR_S0_L001_R1_001.fastq.gz SRR_S1_L001_R1_001.fastq.gz ...
Then tried to run:
cellranger count --id=test --fastqs=fastqgz/ --transcriptome=refdata-gex-mm10-2020-A
which failed with error:
The read lengths are incompatible with all the chemistries for Sample SRR in "/mnt/c/Users/jobac/Downloads/SRA_split_files/GSE104323". - read1 median length = 98 - read2 median length = 0 - index1 median length = 0
I suppose the problem is that I have only one file instead of separate R1,R2,I1. How to obtain them for this dataset or work around this issue ?
Thanks a lot for the help!