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zh3zh / CODA

This is the method CODA(covariation-induced deviation of activity) introduced in the paper "Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity".
MIT License
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SRR to DNA and RNA seuqencing files #1

Open Yijiankai opened 3 years ago

Yijiankai commented 3 years ago

Hi, Could you provide the code on how to convert the original GEO data to 2 DNA sequencing + 2 RNA sequencing files to directly apply your scripts here ? Thanks.

zh3zh commented 3 years ago

Hi, Could you provide the code on how to convert the original GEO data to 2 DNA sequencing + 2 RNA sequencing files to directly apply your scripts here ? Thanks.

Hi, I uploaded gz files of the fastq sequencing data to the repository. Are you talking about how to convert the files you downloaded (sorry, I have no idea about the file format you have atm) to fastq files?

Yijiankai commented 3 years ago

Where are your uploaded fastq gz files? Yes, I am asking how to convert the downloaded files to fastq files since DNA and RNA sequencing are stored in one file. How I can separate them?

zh3zh commented 3 years ago

Where are your uploaded fastq gz files? Yes, I am asking how to convert the downloaded files to fastq files since DNA and RNA sequencing are stored in one file. How I can separate them?

I guess you should follow the guide from SRA (SRA Toolkit) first. Then SplitDNARNAMergedFile.py was used to separate DNA and RNA sequencing data from one file