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rvolden / 10xR2C2

Scripts for analyzing 10x R2C2 data
MIT License
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score.mat #1

Closed hd00ljy closed 3 years ago

hd00ljy commented 3 years ago

Dear Roger,

Thank you for offering a great tool for nanopore scRNA-seq data processing.

I have a few questions regarding the data processing

1. score.mat

in the UMI merging step scores.mat is needed but I cannot find it in this repo and also in C3POa repo where can I find scores.mat file?

2. preprocessing order

I am following the instructions in the repos and the bioarxiv preprint (Highly Multiplexed Single-Cell Full-Length cDNA Sequencing of human immune cells with 10X Genomics and R2C2)

I am planning to execute the code in the following order.

1) C3POa.py 2) C3POa_postprocessing.py 3) ExtractUMIs.py 4) MergeUMIs.py 5) MergeUMIs10x.py 6) detBarcodes.py 7) Demultiplex_R2C2_reads_kmerBased.py 8) match_fastas.py 9) demux_nano.py 10) make_cell_subreads.py

But I am a little bit confusing since the order of scripts are slightly different between that in this repo's README.md and that in the preprint Is merger UMI steps should be done before detBarcodes.py or after all the other scripts?

hd00ljy commented 3 years ago

For 1. score.mat question, scores.mat seems to be not used at all in the code so I'll try running without this option