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Emmanouil "Manolis" Maragkakis, Panagiotis Alexiou <pan.alexiou@gmail.com>
Documentation
A detailed description of CLIPSeqTools
An introduction to CLIPSeqTools
Modules
A collection of tools for the analysis of CLIP-Seq data.
Main CLIPSeqTools application with tools for analysis of CLIP-Seq libraries.
Run all clipseqtools analyses
Assemble reads in clusters and measure their size and number of contained reads distribution
Measure reads at each conservation level
Count reads on transcripts, genes, exons, introns
Measure read distribution on 5'UTR, CDS and 3'UTR.
Measure read distribution on exons and introns.
Export reads to a BED file.
Measure percent of genome covered by reads.
Count reads on genes, repeats, exons, introns, 5'UTRs, ...
Measure Nmer enrichment over shuffled reads.
Measure nucleotide composition along reads.
Measure size distribution of long alignment gaps produced by a gap aware aligner.
Measure size distribution for reads.
A collection of tools to compare two CLIP-Seq libraries.
Run all clipseqtools-compare analyses.
Compare tables with counts.
Perform inner join on tab delimited table files. Can be used to prepare DESeq input file from counts tables.
Count reads of library A that overlap reads in reference library B.
Measure read density around the reads of a reference library
Tools to create plots based on the output of CLIPSeqTools applications.
Create plots for script cluster_size_and_score_distribution.
Create plots for script conservation_distribution.
Create plots for script distribution_on_genic_elements.
Create plots for script distribution_on_introns_exons.
Create plots for script genomic_distribution.
Create plots for script libraries_relative_read_density.
Create plots for script nucleotide_composition.
Create plots for script reads_long_gaps_size_distribution.
Create scatterplot for two tables.
Create plots for script size_distribution.
Tools to process a fastq file with CLIP-Seq data into a database compatible with clipseqtools.
Run all clipseqtools-preprocess analyses.
Annotate alignments in a database table with conservation scores.
Annotate alignments in a database table with deletions.
Annotate alignments in a database table with regions from a BED/SAM file.
Annotate alignments in a database table with genic information.
Keep a single record for multimappers, sort and collapse similar STAR alignments.
Keep a single record for identical sequences
Cut the adaptor sequence from the 3'end of reads.
Load a SAM file in an SQLite database.
Do reads alignment with STAR.
Trim N nucleotides from the start and/or end of FASTQ sequences.
Role to enable reading a GTF file with genes/transcripts from the command line
Role to enable reading a library with reads from the command line
Role to enable output prefix as command line option.
Role to enable plot as command line option
Role to enable reading reference libraries with reads from the command line
Role to enable reading a GTF file with transcripts from the command line
