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-   -   Reptile error correction tool: fastq not readable (http://seqanswers.com/forums/showthread.php?t=26572)

stepa_t 01-16-2013 07:23 AM

Reptile error correction tool: fastq not readable
 
Dear all!
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, despite this file was OK with FastQC and different assemblers. 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?
TIA
Stepan

seb567 02-04-2013 08:59 PM

Quote:

Originally Posted by stepa_t (Post 93923)
Dear all!
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, despite this file was OK with FastQC and different assemblers. 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?
TIA
Stepan

Does the documentation of Reptile say anything about compatibility with FastQ ?

Can you post the result of this:

$ head myFastqFile.fastq


Maybe your reads are too long, who knows.

szimmerman 07-25-2013 07:49 PM

Reptile comes with a program to turn fastq reads into a format it can read. Look at this tutorial for details.

http://aluru-sun.ece.iastate.edu/dok...ptile_tutorial


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