cellranger count help
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19 months ago
shower0617 • 0

enter image description here

these were original data from sequencing company

and then i compressed these files into two files R1 and R2 enter image description here

/data01/chenyu/sc/cellranger-6.1.1/cellranger count \
--id=cellranger_szdxb015 \
--fastqs=/data01/chenyu/sc/sortData/191527A_SZdxb01_5 \
--sample=SZdxb015 \
--transcriptome=/data01/chenyu/sc/refdata-gex-GRCh38-2020-A \
--localcores=20 \
--nosecondary


error occured´╝Ü

FASTQ header mismatch detected at line 4 of input files "/data01/chenyu/sc/sortData/191527A_SZdxb01_5/SZdxb015_S1_L001_R1_001.fastq.gz" and "/data01/chenyu/sc/sortData/191527A_SZdxb01_5/SZdxb015_S1_L001_R2_001.fastq.gz": file: "/data01/chenyu/sc/sortData/191527A_SZdxb01_5/SZdxb015_S1_L001_R1_001.fastq.gz", line: 4

how to fix this problem thanks in advance

cell_cellranger single • 1.2k views
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What code did you use to compress the files?

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I have the same problem, I'll keep you updated if I find anything. Personally I had data issued of a SRA archive, I converted the SRA file with SRA-Toolkit (fastq-dump -I --split-files --gzip), validated the fastqs with ValidateFastq, and had the error.

I also found on this tutorial that the SRA archive issued fastq paired-end files are slightly different and need the usage of the sedcommand. I did all of this and the error still remains.

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