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Old 09-26-2017, 10:14 AM   #1
zauhar
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Location: Philadelphia, PA

Join Date: Oct 2015
Posts: 6
Default 10x genomics and 'paired end' reads

Hi all,

We recently started looking at single cell RNA-seq data produced by our sequencing facility. There were some questions about alignment quality, so I was looking at the fastq read data. The data was generated by 10x genomics library prep (not sure of the specific microfluidic hardware) followed by sequencing on an Illumina machine.

The project PI requested a 'paired end' experiment, and imagined we would have data similar to that provided by a MiSeq experiment, with forward and reverse reads of same length.

Instead, the R2 file has full length reads, and the R1 goes only far enough to capture the cell barcode and UMI (26 bases).

The protocol followed only used 26 cycles for R1. When I questioned why the R1 reads are 'truncated' to minimal length, the manager of the facility basically answers 'that's the 10x protocol'.

We are new to single cell and the 10X platform - is there any reason why more sequence information is not collected on the 'R1' side?

Thanks!
Randy
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