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Old 03-14-2013, 02:35 PM   #1
TabeaK
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Location: Germany

Join Date: Oct 2012
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Default qseq to fastq - post conversion quality trimming

Hiya!

I have a bunch of old RNAseq data sets that I want to re-analyse using our current pipeline. First challenge was that the data is old enough to have been archived in qseq format, not fastq. I converted all files using a neat little java tool found here:

http://sourceforge.net/projects/snpe...q.jar/download

Described here: http://www.biostars.org/p/6682/

Has worked well and is pretty fast. My resulting fastq files, however, contain every single read - including the one with low quality and those that have a failed p/f flag. Therefore I want to some quality trimming before I move on to analysis.

Does anyone have any tool recommendations? And, more importantly, a rational way of filtering? What would be a good quality cutoff to use? If I am not mistaken the quality scores spit out by the java tool are phred64.
Cheers!

TabeaK
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Old 03-15-2013, 05:03 AM   #2
mastal
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Location: uk

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Posts: 667
Default qseq to fastq - post conversion quality trimming

Trimmomatic is good for trimming Illumina data in fastq
format.

http://www.usadellab.org/cms/index.php?page=trimmomatic.

Best wishes,
Maria
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