26 results (0.09 seconds)
Carla Cummins
Documentation
check_tags - check if tr tag is present
check_tags - check if tr tag is present
filter_tags - filter tags at start of fastq sequences
remove_tags - remove user specified tags from start of fastq sequences
run_tradis - Perform full tradis analysis
tradis_plot - Generate plots as part of a tradis analysis
Modules
Bio::Tradis - Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308
Bio::Tradis::AddTagsToSeq - Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.
Bio::Tradis::CommandLine::AddTags - Add given tags to the start of the sequence
Bio::Tradis::CommandLine::CheckTags - Check for presence of tr tag in BAM file
Bio::Tradis::CommandLine::FilterFastqTags - Remove given tags from the start of the sequence
Bio::Tradis::CommandLine::PlotTradis - Generate plots as part of a tradis analysis
Bio::Tradis::CommandLine::RemoveFastqTags - Remove given tags from the start of the sequence
Bio::Tradis::CommandLine::TradisAnalysis - Perform full tradis analysis
Bio::Tradis::CommandLine::TradisBam - Adds tags to sequences if tags are present
Bio::Tradis::DetectTags - Detect tr tags in BAM file
Bio::Tradis::FilterTags - Filter tags in a fastq file
Bio::Tradis::Map - Perform mapping
Bio::Tradis::Parser::Bam - Very basic BAM parser. Limited functionality.
Bio::Tradis::Parser::Fastq - Basic FastQ parser.
Bio::Tradis::RemoveTags - Remove tags from seqs a fastq file
Bio::Tradis::RunTradis - Perform all steps required for a tradis analysis
Bio::Tradis::TradisPlot - Generate plots as part of a tradis analysis



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