Documentation
check if tr tag is present
Perform full tradis analysis
check if tr tag is present
Combine multiple plotfiles and generate updated statistics for the combined files
filter tags at start of fastq sequences
remove user specified tags from start of fastq sequences
Generate insertion site details from TraDIS pipeline plots
Generate plots as part of a tradis analysis
Modules
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
Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.
Custom exceptions
Take in a bam file and plot the start position of each read
Combine multiple plotfiles and generate updated statistics for the combined files
Add given tags to the start of the sequence
Check for presence of tr tag in BAM file
Remove given tags from the start of the sequence
Combine multiple plotfiles and generate updated statistics for the combined files
Generate plots as part of a tradis analysis
Remove given tags from the start of the sequence
Perform mapping
Perform full tradis analysis
Adds tags to sequences if tags are present
Detect tr tags in BAM file
Exceptions for input data
Filter tags in a fastq file
Perform mapping
Very basic BAM parser. Limited functionality.
Take in a cigar string and output start and end relative to the reference sequence
Basic FastQ parser.
Remove tags from seqs a fastq file
Perform all steps required for a tradis analysis
Change samtools syntax depending on version found
Generate plots as part of a tradis analysis