error correction for RNA-seq reads

[fhb]

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

[bioinfosm]

What kind of error correction you are referring to?

[fhb]

wrong nucleotide call from the sequencing machine.

[NicoBxl]

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 )

[fhb]

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

[NicoBxl]

here's a an example of workflow to trim bad quality tails with R

http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Trimming-Low-Quality-3-Tails-from-R

[bioinfosm]

thats an awesome collection from UCR!