Question: Run Cellranger Count with Novogene fastq files
0
gravatar for rf3x
8 weeks ago by
rf3x0
rf3x0 wrote:

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!

sequencing rna-seq alignment • 154 views
ADD COMMENTlink modified 8 weeks ago by swbarnes27.8k • written 8 weeks ago by rf3x0
1

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.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by igor10k

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 \
ADD REPLYlink modified 8 weeks ago by ATpoint35k • written 8 weeks ago by rf3x0

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

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Diedes20
0
gravatar for swbarnes2
8 weeks ago by
swbarnes27.8k
United States
swbarnes27.8k wrote:

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

ADD COMMENTlink written 8 weeks ago by swbarnes27.8k
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