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rvolden / 10xR2C2

Scripts for analyzing 10x R2C2 data
MIT License
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How is "R2C2_10x_postprocessed.fasta" generated? #6

Open johnchamberlin opened 3 years ago

johnchamberlin commented 3 years ago

Hi, I am trying to understand the workflow but it appears to begin with a "postprocessed" fasta rather than what I can download from SRA. How do I generate the "R2C2 reads and R2C2 10x reads" (as described in README)? I.e. is the 10x cell barcode/UMI always the first 26bp of the R2C2 read, or is the orientation sometimes reversed?

thank you,

rvolden commented 3 years ago

Postprocessed reads refers to reads generated from my C3POa pipeline. It's also worth noting that none of these scripts (or C3POa for that matter) are supported anymore since I graduated a few months ago.

yollct commented 1 year ago

Hi, I am trying to understand the workflow but it appears to begin with a "postprocessed" fasta rather than what I can download from SRA. How do I generate the "R2C2 reads and R2C2 10x reads" (as described in README)? I.e. is the 10x cell barcode/UMI always the first 26bp of the R2C2 read, or is the orientation sometimes reversed?

thank you,

Hi @johnchamberlin @rvolden , I think its a bit late, but I am now trying to work on this dataset. I guess the R2C2 reads are the consensus reads and R2C2 10x reads are the barcodes from 10x (if I am correct..).

I am wondering if you had successfully preprocess this data? I am a bit confuse with the splint used in the paper, as it provided two splints. So after running C3POa, I got two consensus files for each splint per sample. Question is: which one should I use? Or should I merge them? I tried to look for the answer, but the paper didn't say much about the two splints. Any help will be very much appreciated. Thank you!!

Best Chit Tong