I've tried to use Reprile error correction tool ( http://aluru-sun.ece.iastate.edu/doku.php?id=reptile ) for my MiSeq reads, but unfortunately this soft cannot read my fastq file. Do you know if there is any modification in fastq format in MiSeq versus other Illumina sequencers, since supposedly it was tested only on GA data? Is there any FastQ file converters?
There is a Perl script in the REPTILE package (v1.1 update) called ./fastq-converter.pl to do what you need.
Here are the information from the REPTILE README file:
"Short read data are typically stored in .fastq files. A Perl script is
provided to convert Fastq files to .fa (sequence) and .q (quality) files, the
format required by Reptile. This script also provides options for
preprocessing and filtering the data. This script is located at
'./utils/fastq-converter-v2.0.pl'."
You've got further information about its usage in the same README file
Really old question, but could help ...
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