📦 bio-tradis

36 pages

A

add_tradis_tags(1p)check if tr tag is present✨

B

bacteria_tradis(1p)Perform full tradis analysis✨
Bio::Tradis(3pm)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(3pm)Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.✨
Bio::Tradis::Analysis::Exceptions(3pm)Custom exceptions✨
Bio::Tradis::Analysis::InsertSite(3pm)Take in a bam file and plot the start position of each read✨
Bio::Tradis::CombinePlots(3pm)Combine multiple plotfiles and generate updated statistics for the combined files✨
Bio::Tradis::CommandLine::AddTags(3pm)Add given tags to the start of the sequence✨
Bio::Tradis::CommandLine::CheckTags(3pm)Check for presence of tr tag in BAM file✨
Bio::Tradis::CommandLine::FilterFastqTags(3pm)Remove given tags from the start of the sequence✨
Bio::Tradis::CommandLine::PlotCombine(3pm)Combine multiple plotfiles and generate updated statistics for the combined files✨
Bio::Tradis::CommandLine::PlotTradis(3pm)Generate plots as part of a tradis analysis✨
Bio::Tradis::CommandLine::RemoveFastqTags(3pm)Remove given tags from the start of the sequence✨
Bio::Tradis::CommandLine::RunMapping(3pm)Perform mapping✨
Bio::Tradis::CommandLine::TradisAnalysis(3pm)Perform full tradis analysis✨
Bio::Tradis::CommandLine::TradisBam(3pm)Adds tags to sequences if tags are present✨
Bio::Tradis::DetectTags(3pm)Detect tr tags in BAM file✨
Bio::Tradis::Exception(3pm)Exceptions for input data✨
Bio::Tradis::FilterTags(3pm)Filter tags in a fastq file✨
Bio::Tradis::Map(3pm)Perform mapping✨
Bio::Tradis::Parser::Bam(3pm)Very basic BAM parser. Limited functionality.✨
Bio::Tradis::Parser::Cigar(3pm)Take in a cigar string and output start and end relative to the reference sequence✨
Bio::Tradis::Parser::Fastq(3pm)Basic FastQ parser.✨
Bio::Tradis::RemoveTags(3pm)Remove tags from seqs a fastq file✨
Bio::Tradis::RunTradis(3pm)Perform all steps required for a tradis analysis✨
Bio::Tradis::Samtools(3pm)Change samtools syntax depending on version found✨
Bio::Tradis::TradisPlot(3pm)Generate plots as part of a tradis analysis✨

C

check_tradis_tags(1p)check if tr tag is present✨
combine_tradis_plots(1p)Combine multiple plotfiles and generate updated statistics for the combined files✨

F

filter_tradis_tags(1p)filter tags at start of fastq sequences✨

R

remove_tradis_tags(1p)remove user specified tags from start of fastq sequences✨

T

tradis_comparison(1)bio-tradis: compares two experimental conditions using the method of Dembek et al.✨
tradis_essentiality(1)bio-tradis: produces calls of gene essentiality using an adaptation of the method described in Langridge et al.✨
tradis_gene_insert_sites(1p)Generate insertion site details from TraDIS pipeline plots✨
tradis_merge_plots(1)bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R✨
tradis_plot(1p)Generate plots as part of a tradis analysis✨