![]() Traditional alignment methods such as BLAST cannot be used for large data sets generated by NGS as they are too memory consuming. Therefore, it is crucial to remove reads that are too short prior to performing the alignment as misaligned reads will lead to false-positive variant calls. Paired-end reads reduce this issue since a pair of reads has a known distance in between which is used to validate its alignment position. Table 1 : Summary of the different file types used in NGS Data analysisĪ problem that persists in NGS is that short reads can sometimes align equally well to multiple locations in the genome, the longer the read the easier it is to find its position. The Variant Call Format is a text file which stores sequence variants, each variant occupies a single row Used for input into variant calling pipelines Can be opened in genome browsers to view read alignment position and qualityīinary Alignment Map file is a compressed binary version of a SAM file. ![]() Store information on read alignment, e.g. Sequence Alignment Map file, used to store text-based information for reads aligned to a reference sequence In variant calling pipelines to direct the analysis to a genomic region Storage of raw sequence data and input into sequence alignmentīrowser Extensible Data file is a tab-delimited text file that is used to store genomic regions as coordinates Text-based file format containing raw sequence reads and the associated quality score of each base
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