Hi Biostars,

I've downloaded some scRNA-Seq data from the GSA, which I am hoping to analyze. This is 10x V2 chemistry sequence data.

However the format is different from what I am familiar with. First, the reads come in 2 fastq files ("f1" and "r2"):

CRR034505_f1.fastq.gz
CRR034505_r2.fastq.gz

More importantly, both mates have equal read lengths:

zcat CRR034505_f1.fastq.gz | head -n4
@ST-E00126:655:HL5FTCCXY:5:1101:7638:1151 1:N:0:NAAGTGCT
NAGTAACCAAGACACGTATTGCGCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAACTAAAAAGGGGTCCCAGAATTTCAGCAGTTCTCTGATTTTTATATTTTATTCCTCTTCCTATCCAATCCCTGCCTTTTGCTTCAAGGTG
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAA--7<<--AFFJ7-)-7)--<AAF7<<--7-----77---AA7AFJF7F<A----7A-<-AA<F<A7-A-77)--<F-<<--7A--<-77

zcat CRR034505_r2.fastq.gz | head -n4
@ST-E00126:655:HL5FTCCXY:5:1101:7638:1151 2:N:0:NAAGTGCT
NCAAAGAAAAAGACACATTTGGGAAGAAAAGCAGGAAAAACGTTAAAGAAAATGTACTTACCACCTGGACTCAAAAGGCAGGGATTGGATAGGAAGAGGAATAAAATATAAAAATCAGAGAACTGCTGAAATTATGTGACCACTTTTTAG
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJAJJJJFJJFAJFJJJJJJJJJJJJJJJJJJF-A7JAAF---7<<AFJFF<AJ--F-)-7<<FJAFA

I have never seen a scRNA-Seq data set that looks like this, though I have not done much work with 10x V2 chemistry in the past.

Is this normal? Has anybody encountered scRNA-Seq data like this before?

Thanks!

Dave