Hello!

I am new to processing snRNAseq data, and am going through the 10X cellranger pipeline.

I could not find any bam files to download from the SRR numbers, so I chose to process raw fastq files.

This is how I downloaded the files, using 1 as an example:

1. prefetch SRA files

prefetch SRR9141212

1. Fastq-dump zipped files

   fastq-dump --split-3 --skip-technical --readids --read-filter pass --gzip /project/nilslind_369/cfausto/wilson-diabetes/input/pretrim/SRR9141212.sra

2. Rename the two fastq.gz files to match cellranger count nomenclature (moved into one directory)>

   mv SRR9141212_pass_1.fastq.gz ctrl1_S1_L001_R1_001.fastq.gz

SRR9141212_pass_2.fastq.gz ctrl1_S1_L001_R2_001.fastq.gz

1. Script for cellranger count

   cellranger count --id=ctrl1 \ --transcriptome=/project/nilslind_369/cfausto/Ref_Genome/hg38/Homo-sapien_genome \ --fastqs=/project/nilslind_369/cfausto/wilson-diabetes/input/ctrl1

Here is the error message when the job fails early on:

FASTQ header mismatch detected at line 4 of input files "/project/nilslind_369/cfausto/wilson-diabetes/input/ctrl1/ctrl1_S1_L001_R1_001.fastq.gz" and "/project/nilslind_369/cfausto/wilson-diabetes/input/ctrl1/ctrl1_S1_L001_R2_001.fastq.gz": file: "/project/nilslind_369/cfausto/wilson-diabetes/input/ctrl1/ctrl1_S1_L001_R1_001.fastq.gz", line: 4

When I head the fastq file, it looks like it's in the wrong format:

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I'm not sure why it looks like this, maybe because it's a zipped file? Any different way to get the fastq files would be greatly appreciated!