Run Cellranger-ATAC on CNGB fastq files
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8 weeks ago
TomCat • 0

I'm trying to run cellranger-atac(2.1.0) from dataset of this article: https://www.cell.com/cell-reports/fulltext/S2211-1247(22)00765-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124722007653%3Fshowall%3Dtrue

I have downloaded G3 stage fastq files from here (https://db.cngb.org/search/run/CNR0183377/) and renamed file names like;

V100011106_S1_L001_R1_004.fastq.gz V100011106_S1_L004_R2_001.fastq.gz

Then I ran cellranger-atac like;

$ cellranger-atac count --id V100011106_L04 --reference /path/to/reference --fastqs /path/to/fastqs

and I got following error message;

Log message:
Unable to read barcode sequence for read ID V100011106L4C001R0010000003/1: there was no I2 read FASTQ and we were unable to read a 16-base barcode from the FASTQ header. Make sure that the flow cell was demultiplexed correctly.

I think this is due to renamed fastq header in the database. But I couldn't find I2 fastq file from the repository, and I can't use "fastq-dump --origfmt" or "fastq-dump --split" command because this database is not SRA. How can I fix this?

I'm using cellranger-atac (2.1.0) on Ubuntu 22.04.3 LTS on wsl2 of windows11.

Cellranger-ATAC CNGB • 319 views
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Can you find these samples in SRA by any chance? That would be the way to go, if the read headers are renamed oddly.

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Thank you for your reply. I think that these data are note registered in SRA because I couldn't find any files when I searched by "Branchiostoma floridae single cell atac" or "CNR0183377" in SRA.

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