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Old 01-16-2013, 07:23 AM   #1
stepa_t
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Location: Kaliningrad

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Default 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
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Old 02-04-2013, 08:59 PM   #2
seb567
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Location: Québec, Canada

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Quote:
Originally Posted by stepa_t View Post
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.
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Old 07-25-2013, 07:49 PM   #3
szimmerman
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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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