Also, we have put emphasis on improving the transcript coverage and gene completeness so that it can be of wide use for gene prediction, even in highly polymorphic genomes.
In order to improve the fusion transcripts, we decided to split them.
Undoubtedly the availability of additional EST and genome sequence data will improve the reliability of transcript identification.
Unlike de novo assembly algorithms such as Trinity, Tiling Assembly takes advantage of a sequenced genome to improve the accuracy of transcript assembly while decreasing CPU requirements.
Bias detection and correction to improve the accuracy of transcript abundance was used by supplying a multi fasta file of E. grandis genome.
Our procedure to handle evidence introns as implemented in ASPic-GeneID is also expected to improve the accuracy at the transcript level.
To reduce the coverage of highly expressed genes and to improve the ability to assemble transcripts and transcript isoforms originating from lowly expressed genes, k-mers (k = 25) from quality filtered Illumina paired end reads were reduced to ≤ 30X coverage using digital normalization [ 72].
Mapping of 3' reads with a length of more than 26 nucleotides did not substantially improve the ratio of transcripts that aligned to both the human and the SL1344 transcriptome as can be inferred from the numbers of reads excluded during multi-step annotation.
Transcriptome reconstruction was performed using uniquely mapped reads or, alternatively, all the reads (unique and repeated) in order to improve the identification of the transcripts that are duplicated in the P. profundum genome like for example the CRISP elements and to better define the transcript structure of the genes having repeated regions.
Because of co-transcription of genes within an operon, borrowing information from other genes within the same operon can improve the estimation of relative transcript levels; the estimation of relative levels of transcript abundances is one of the most challenging tasks in experimental genomics due to the high noise level in microarray data.
