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Forum: Illumina/Solexa 09-26-2017, 11:53 AM
Replies: 8
Views: 8,523
Posted By zauhar
Yes, they did do the whole analysis, including...

Yes, they did do the whole analysis, including generation of alignments, counts and clustering.

I have also installed cellranger on my own server so I can better understand their pipeline.
Forum: Illumina/Solexa 09-26-2017, 10:42 AM
Replies: 8
Views: 8,523
Posted By zauhar
This may answer my own question - the facility...

This may answer my own question - the facility manager sent a followup: the 10X library prep involves a 30nt poly-T section after the barcode/UMI, and he indicates that the 10X analysis software will...
Forum: Illumina/Solexa 09-26-2017, 10:14 AM
Replies: 8
Views: 8,523
Posted By zauhar
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....
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