The ratio was well preserved through the initial amplification and after post-processing filtering to exclude problematic sequences and to trim error-prone ends.
An important development for the future is to develop and utilise more precise methods to control for these biases in bioinformatics pipelines (including base calling, read trimming, error correction and mapping algorithms).
Furthermore, the trimming errors were distributed over various vectors.
This high percentage of true miRNAs showed that inefficient amplification, sequencing or trimming errors did not affect our experiment [ 45].
If a major part of the library was affected by inefficient cloning, sequencing or trimming errors, majority of the conserved miRNAs will be outside the 20 24 nt range.
The trimming errors with this program would occur if the size of the cDNA insert was so small that the start of the vector fell into the critical 30% range from either end of the EST sequences.
If data in such giant projects were incompletely trimmed, errors that existed in the data from other small projects may be overwhelmed and become invisible in the sampled data.
Some assemblers, such as ALLPATHS-LG (Gnerre et al. 2011), where trimming and error correction are performed within the assembly pipeline, even require raw reads, without quality trimming as input.
In addition, the framework already provides several algorithms to perform some of the standard steps in the assembly pipeline (e.g., Trimming, Overlapping, Error Correction, Scaffolding, Validation).
By providing Phrap with trimmed and error-corrected reads, we reduce the possibility of errors in Phrap consensus.
On the basis of trimmed and error-corrected Illumina sequences, we corrected the sequencing errors within all contigs initially assembled from the Roche 454 reads.
