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TUTORIAL: Transcriptome Assembly Read correction

June 17, 2019 Next page

3. Correct errors in trimmed RNAseq reads using Rcorrector

• corrects reads based on frequencies of trusted k-mers
  
• computes a local threshold for read correction at each position in a read
  
• scales well with respect to memory for larger datasets by storing only k-mers that occure more than once in a read set
  

Output from Trimmomatic will have the .fq file extension, so choose Yes for Only process... and enter the P.fastq file extension. This will select only the paired reads, ignoring the unpaired reads.

Clicking on Run will bring up a new blreads window with the best quess of file pairing, in two columns. Usually, guesspairs.py gets it right. Files for which a pair cannot be found (ie. single-end reads) would be listed in a single column. To run Rcorrector with these read pairs, choose Edit --> SelectAll, and then Reads --> Rcorrector.

By default, Rcorrector will write corrected reads to a directory in the parent directory (ie. not within reads.trimmed) called reads.trimmed.Rcorrector. Let's change that to reads.Trimmomatic.Rcorrector. Rcorrector may take awhile to run, so you may wish to set "Notify of completion by email" to Yes and type in an email address. (On this dataset, Rcorrector took about 8 min. to complete using 16 threads.)

The output is written to the reads.Trimmomatic.Rcorrector directory, whose contents is shown at right.