Welcome to split_library_log_parser’s documentation!¶
Author: Menachem Sklarz
Date: 24/1/2017
Why should I need this?¶
When using QIIME, one of the first steps is the split_libraries_fastq.py
script which performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files, while also doing some basic quality testing.
This step creates a log file, split_library_log.txt, which contains statistics about the number of reads per sample that passed the various tests and manipulations.
parse_split_library_log.R
converts this text file into a tsv table, which is more convenient for comparison between the samples etc.
Usage¶
Simple! Just execute the following::
Rscript parse_split_library_log.R \
--input split_library_log.txt \
--output split_library_log.tsv
Where:
--input file | Path to split_library_log.txt |
--output file | Path to tab-delimited output file |
Dependencies¶
Please make sure you have the following libraries installed in your R version:
- magrittr
- optparse
- tools