Please consult these tutorials for more specific information on each mapping program. ![]() Previous versions of this class and tutorial have covered using bowtie and bwa. More will be discussed about selecting a good tool on Friday. It is possible a different read mapper would be better for your set of experiments. Each mapper has its own set of limitations (on the lengths of reads it accepts, on how it outputs read alignments, on how many mismatches there can be, on whether it produces gapped alignments). Things seem to have reached the point where there is mainly a trade-off between speed, accuracy, and configurability among read mappers that have remained popular. There are over 50 read mapping programs listed here. The world of read mappers is settling down after being a bioinformatics Wild West where there was a new gun in town every week that promised to be a faster and more accurate shot than the current record holder. In this tutorial we'll explore these basic principles using bowtie2 on TACC. ![]() ![]() ![]() Once you know you are working with the best quality data ( Evaluating Raw Sequencing data tutorial) possible, the first step in nearly every NGS analysis pipeline is to map sequencing reads to a reference genome.
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