Easiest way to install PEAR is through Anaconda
And the following to install the needed package:
conda install -c bioconda pear
- ./data/VH3-53_RBD_antibodies.tsv: List of IGHV3-53/3-66 RBD antibodies from literatures
- ./data/IGKV1-9_CDRH3.txt: List of CDR H3 from IGHV3-53/3-66 RBD antibodies that pair with IGKV1-9
-
categorize antibodies based on CDR H3 length and light chain germline
- run python script
script/summarize_LC_vs_CDRH3_length.py
- run R script
script/plot_LC_vs_CDRH3_length.R
for plotting
- run python script
-
analyzing SHM for antibodies with different CDR H3 length
- run python script
script/format_SHM_table.py
- run R script
script/plot_SHM_heatmap.R
for plotting
- run python script
-
merge overlapping paired-end reads
- pear -f [READ1 FASTQ FILE] -r [READ2 FASTQ FILE] -o fastq/S10
-
run analysis for the assembled files
- run python script
script/fastq2count.py
to count the frequence of each variant of CDRH3 loop - run python script
script/merge&calculate.py
to calculate the relative enrichment of each variant
- run python script
-
plotting results
- run R script
script/plot_yeast_display.R
- run R script