Run Cellranger Count with Novogene fastq files

Question

[rf3x]

Hello! Can anyone who have experience with analysis of Novogene fastq files via Cellranger Count give me some suggestion? The files from Novogene seem not recognize by Cellranger Count. Wha shall I do? Thank you so much!

[igor]

Can you post what kind of files you are starting with and what command you are using?

For example, you could be doing everything right, but you just have a typo somewhere.

[rf3x]

The following the structure of fastq files:

-

rw-r--r-- 1 rf3x users 20210055171 Apr  2 13:14 DVC1_CKDL190145170-1a-SI_GA_A1_HTCTKDSXX_L4_1.fq.gz
-rw-r--r-- 1 rf3x users 17381988826 Apr  2 13:07 DVC1_CKDL190145170-1a-SI_GA_A1_HTCTKDSXX_L4_2.fq.gz
-rw-r--r-- 1 rf3x users  1485512248 Apr  2 13:11 DVC1_CKDL190145170-1a-SI_GA_A1_HTCTKDSXX_L4_I1.fq.gz

The script that I used is the following:
cellranger count \
--id=DVC1 \
--fastqs=/scratch/rf3x/Novogene/DVC1 \
--sample=DVC1 \
--transcriptome=/scratch/rf3x/Novogene/Mus_musculus.GRCm38.98.premrna.filtered \
--expect-cells=10000 \
--jobmode=local \
--localcores=8 \
--localmem=72 \

[Diedes]

What is the output of zcat DVC1_CKDL190145170-1a-SI_GA_A1_HTCTKDSXX_L4_* | head -n 8

Answer 1

[swbarnes2]

Cellranger is very fussy about the names of the fastqs. They have to be just as mkfastq or bcl2fastq would name them, and yours are not right.. They need to be in the form of "mysample_S1_L001_I1_001.fastq.gz"

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input