A surprising number of analyses require that we compute genome or interval coverages.
Half-sequence and half mythical-beast, "unaligned" BAM files are used to store FASTQ files.
The recipe attempts the find the most similar matches to a "mystery 16S sequence".
The recipe demonstrates the effect of using different tasks may have on finding hits.
Perform data quality control on FASTQ data
The recipe produces pairwise alignments with different software
Visualizing large scale genomic variations.
Use SAM flags to make scientific discoveries. (work in progress)
This recipe follows the variant calling process in the Biostar Handbook.
Filtering Sequence Alignment Maps (SAM/BAM) files.
Bacterial variant caller
The recipe demonstrates the use of different short read aligners.
This recipe evaluates SNP callers on a the syndip data.
Your mission, should you choose to accept it, is to reproduce major findings of a Science paper in just 60 seconds.
RNA-Seq differential expression with alignments and using three different statistical methods.
The recipe demonstrates the utility of blast databases for manipulating sequences.
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