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Old 11-16-2010, 12:51 PM   #1
fhb
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Default error correction for RNA-seq reads

Hi everyone,

can someone share any experience using error correction for RNA-seq reads. I am reluctant to use it since I have not seen any paper using the available tools.

Thanks,
Fernando
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Old 11-16-2010, 02:33 PM   #2
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What kind of error correction you are referring to?
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Old 11-16-2010, 02:40 PM   #3
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wrong nucleotide call from the sequencing machine.
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Old 11-17-2010, 12:23 AM   #4
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in you're fastq file, you've an information of the quality of the base calling. You can filter the reads with a bad quality with a little perl script per example ( or with R too )
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Old 11-17-2010, 07:07 AM   #5
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Quote:
Originally Posted by NicoBxl View Post
in you're fastq file, you've an information of the quality of the base calling. You can filter the reads with a bad quality with a little perl script per example ( or with R too )
I am glad you wrote this because that is the approach that I've been taking: filtering reads with overall bad quality and trimming bad quality bases.

This is the reason I wanted to know if people have done error correction, and if it has improved their percentage or aligned reads better then trimming nucleotides on the basis of the quality of the call.

thanks very much,
Fernando
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Old 11-17-2010, 11:55 PM   #6
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here's a an example of workflow to trim bad quality tails with R
http://manuals.bioinformatics.ucr.ed...3-Tails-from-R
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Old 11-18-2010, 02:58 PM   #7
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thats an awesome collection from UCR!
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