Is there any tutorial for Following:
- how to download Fastq file from NCBI
- how to check the file quality (How they needs to be?)>
- How to use cell ranger count on Fastq file?
- How to understand the output of the count?
I want to work with the healthy data set from the following website:
I downloaded the fastq file using following command:
fastq-dump --split-files --gzip SRR10134390
I downloaded the reference from Gencode and make ref for cellranger count using following command
mkref --genome=GRCh38.p13 --fasta=GRCh38.primary_assembly.genome.fa --genes=gencode.v39.primary_assembly.annotation.gtf
I ran the cellranger count using the following command:
cellranger count --id=Healthy_aortic_valve2 --fastqs=/healthy1 --transcriptome=GRCh38.p13 --chemistry SC3Pv2
This commands run and created several folders but it does not seem right . because I can not find matrix files, and or BAM files.
Can someone tell me how I can find out the problem?