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TUTORIAL: Transcriptome Assembly

Read correction


  June 17, 2019

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References


Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
Li Song Liliana Florea
GigaScience, Volume 4, Issue 1, 1 December 2015, s13742-015-0089-y, https://doi.org/10.1186/s13742-015-0089-y



3. Correct errors in trimmed RNAseq reads using Rcorrector

Rcorrector offers a number of improvements over previous methods for correcting RNA sequencing reads:
The goal is to perform error correction on the trimmed read files (_val_x_fq.gz) from the previous step. If you closed the blreads window, simply start another instance of blreads in the reads.Trimmomatic directory.



As done in the previous section, choose File --> guesspairs.py.
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.







Next: Assembly of RNA transcripts