Some scripts for parsing NGS data from: Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality
-
script/Mapper1.py: Mapping and calling mutations
- Input:
- raw sequencing reads in fastq format
- Fasta/flu3amp.fa
- raw sequencing reads in fastq format
- Output: result/AllM_3
- Input:
-
script/Mapper2.py: Filter clones with >1 mutations and generating a table that contains amino acid information
- Input:
- Fasta/flu3offset
- Fasta/BarCode
- result/AllM_3
- Fasta/flu3info
- Fasta/flu3offset
- Output:
- result/WT_N_Depth
- result/AGenotypes
- result/SGenotypes
- result/SMut'
- result/WT_N_Depth
- Input:
-
script/Mapper3.py: Generate a table only containing mutations with high confidence in fitness estimation (high input frequency)
- Input: result/SMut
- Output: result/HCMut
- tmp/sil
- tmp/mis
- tmp/non
AN UPDATED VERSION OF Mapper1.py AND Mapper2.py CAN BE FOUND IN REPOSITORY: https://github.com/wchnicholas/lib240