/count_dual_indexes

C++ program to take the FASTQ files of two indexes and count the index pairs.

Primary LanguageC++MIT LicenseMIT

count_dual_indexes

C++ program to take the FASTQ files for two indexes and count the index pairs. Could be useful if you don't get the expected ratio of counts for demultiplexing or have other issues with the pair content of your output. Relatively speedy.

Installation

Requires Makefile and a g++ compiler capable of using the C++11 standard.

make

This will compile the count_dual_indexes program, which can be copied to your user path for standard usage.

Example usage

Standard FASTQ files, minimum 1000 reads to print a pair, print to standard out.

count_dual_indexes --index1 my_run_R2.fastq --index2 my_run_R3.fastq --threshold 1000

Standard FASTQ files, minimum 1000 reads to print a pair, print to file.

count_dual_indexes --index1 my_run_R2.fastq --index2 my_run_R3.fastq --threshold 1000 1>index_counts.tsv 2>errors.log

Bash environment, gzip FASTQ files (use process substitution), minimum 100,000 reads to print a pair, print to file. Run with no-hangup and in the background.

nohup count_dual_indexes --index1 <(gunzip -cd my_run_R2.fastq.gz) --index2 <(gunzip -cd my_run_R3.fastq.gz) --threshold 100000 1>index_counts.tsv 2>errors.log &