|News and Announcements »|
The ERA currently requires a separate FASTQ file for each library, split by library id. This code takes the output from split_libraries.py and the corresponding QUAL files and produces ERA-compatible FASTQ files.
Usage: make_fastq.py [options]
Matches QUAL info to FASTA entries by id, and writes FASTQ output to one file or to per-library files.
The FASTQ format for each record is as follows:
@seq_id [and optional description] seq as bases + [and optionally with repeat of seq_id and repeat line] qual scores as string of chr(33+qual)
Take input FASTA file input_fasta_filepath and QUAL file input_qual_filepath: make separate file for each library (with the -s option: assumes that the FASTA file is the output of split_libraries.py or similar script):
make_fastq.py -f $PWD/seqs.fna -q $PWD/Fasting_Example.qual -s