Hello everyone,
I download a single fastq.gz file from a study posted on GEO, and this is a paired read single cell sequencing. Somehow this study compressed R1 and R2 file into one fastq.gz file, I used zcat to check the reads and they are really long, like 98 characters. I want to split them to a R1_fastq.gz and R2_fastq.gz files. Please give me some advice on what should I do.
1 answer
Looks like this is a 10x dataset which can be a hit-or-miss proposition to download intact from SRA. Your best bet is to either use the count file provided in the GEO record or use Data Access tab to download the bam format file that has original data https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR10254549&display=data-access . Then use bam2fastq utility provided by 10x to reconstruct the original fastq data.
You can use wget with the link https://sra-pub-src-2.s3.amazonaws.com/SRR10254549/SC2possorted_genome_bam.bam.1
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Can you post the accession number so we can examine the record? From where and how did you download the file?
Hi, thanks for your replay. I download this study: GSE138669 from GEO. I used download link generated by SRA explorer using ascp download the fastq.gz.
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