CLIP-seq data analysis bioinformatics software tools

Cross-Linking Immunoprecipitation associated to high-throughput sequencing (CLIP-seq) is a technique used to identify RNA directly bound to RNA-binding proteins across the entire transcriptome in cell or tissue samples. Recent technological and computational advances permit the…

CLIP-seq analysis steps

Most recent bioinformatics tools

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SureMap
Desktop

SureMap

Handles reads requiring special attention during read mapping. SureMap can map…

Handles reads requiring special attention during read mapping. SureMap can map short and long reads to a reference genome and outputs a list of all possible locations within any given edit distance…

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ISEA
Desktop

ISEA Iterative Seed-Extension Algorithm

Provides an iterative seed-extension algorithm for de novo assembly. ISEA…

Provides an iterative seed-extension algorithm for de novo assembly. ISEA comports five steps: (i) preprocessing, (ii) graph and seed building, (iii) contig extension, (iv) merging and (v)…

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SOAPaligner
Desktop

SOAPaligner Short Oligonucleotide Analysis Package

Enables ultrafast and memory-efficient alignment of massive short sequencing…

Enables ultrafast and memory-efficient alignment of massive short sequencing reads. SOAPaligner permits users to index the reference and perform reads alignment. It can tolerate as low as 60 per cent…

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DeDup
Desktop

DeDup

Removes duplicate merged reads on single end data. DeDup can be applied to…

Removes duplicate merged reads on single end data. DeDup can be applied to forward, reverse and merged reads. It retains a single read for a given genomic position and read direction to deduplicate…

Most popular analytical software

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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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Bowtie
Desktop

Bowtie

A short read aligner that aligns short DNA sequences (reads) to the human…

A short read aligner that aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its…

ZENBU
Web

ZENBU

Enables data exploration through "on-demand" data processing and…

Enables data exploration through "on-demand" data processing and interactive linked-visualizationsthus enabling concurrent views from the same mere primary sequence alignment data which…

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Trimmomatic
Desktop

Trimmomatic

Performs a variety of useful trimming tasks for illumina paired-end and single…

Performs a variety of useful trimming tasks for illumina paired-end and single ended data.

Curators for CLIP-seq analysis

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