How to set cellranger parameters?

[liguowei-CAS]

Hi Loyale,

Thanks for your nice work about mouse retina! I'd like to explore these data for my study, but I am confused with them.

1. After download and fast-dump sra file from GSE118614, I only got one gz file per sample, which typically should outcome two or three gz files (R1, R2, and I1), right?
2. I guessed they were sequenced by 10x Genomics v1 library, so, one gz file is reasonable. But I got stuck in cellranger settings and had no meaningful output. Here is my command line used:

➜  GSE118614 tree | grep E11
├── E11.fastq.gz
├── E11_S1_L001_R1_001.fastq.gz -> E11.fastq.gz
├── E11.sra

/software/cellranger-1.1.0/cellranger run --id=E11 --fastqprefix=E11 --fastqs=./ --transcriptome=/reference/mouse/mm10/GENCODEvM25.cellranger.1.1.0
and
/software/cellranger-3.0.2/cellranger count --id=E11 --fastqs=./ --sample=E11 --transcriptome=/reference/mouse/mm10/GENCODEvM25

May I know your command line about cellranger setting about these samples? Thanks a lot !

Regards,
guowei

[liguowei-CAS]

Here is the reply from Prof. Clark in email:

_I would download the raw files that we uploaded. Within the websites the original .bam files are available. For some reason when they converted the bam file to a fastq, they only did single end reads. Instead, I would convert the bam files to fastq using samtools.

Also, this data was all using 10x 3’ v2 reagents._

For those who may need it. Thanks Prof. Clark again.