Deep Sequencing Data Analysis: Challenges and Solutions

Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges

“…After sequencing, one or more text files are produced in the fasta, fastq or csfasta, and qual formats, depending on the equipment settings and platform used. These files contain the nucleotides sequenced for each read and a quality score for each base/color call (Isakov and Shomron, 2011). Usually, the sequencer manufacturer provides software able to process this data in the very beginning steps toward publication.…”

“…This can be a computationally demanding task due to the great volume of short sequences produced and also nucleotide and structural variance, sequencing errors, RNA editing, and epigenetic modifications (Isakov and Shomron, 2011), especially for the traditional alignment tools (Lee et al, 2011). Hence, a new generation of short read aligners has been developed, saving computational time by indexing the read sequences, or the genome prior alignment (Lee et al, 2011).…”

“…Hence, a new generation of short read aligners has been developed, saving computational time by indexing the read sequences, or the genome prior alignment (Lee et al, 2011). Several aspects of the aligner must be considered: memory and time requirements and limitations, and how the tool is adequate to the task (Isakov and Shomron, 2011). For instance, many short read aligners can be programmed to return the results of the reads whose first part perfectly matches the reference genome, which allows to search for potential isoforms of miRNA (Motameny et al, 2010).…”

“…In this direction, the Novoalign software has a special option to align miRNA in which it searches for regions complementary to the reads near the mapped loci (Hercus, 2008). Most sequence aligners generate results in the sam file format which can be processed by the SAMtools kit (Li et al, 2009c; Isakov and Shomron, 2011). One thing worth noticing is that when a short sequence is aligned to a large and complex genome with repetitive regions, such as the human genome, is expected to find reads mapped in multiple locations in the genome (McCormick et al, 2011).…”