<commit_before><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<head><title>Chipster manual</title></head>
<body>

<h2>Analysis tools for next generation sequencing data</h2>
			

<p>Chipster's NGS analysis tools are grouped in the categories listed below. Chipster also contains a <a href="genomeBrowser.html">built-in genome browser</a>,
allowing you to view reads and results in their genomic context.</p>

<ol>
<li> <a href="#quality">Quality control</a> </li>
<li> <a href="#preprocessing">Preprocessing</a> </li>
<li> <a href="#utilities">Utilities</a> </li>
<li> <a href="#regions">Matching genomic regions</a> </li>
<li> <a href="#alignment">Alignment</a> </li>
<li> <a href="#variants">Variants</a> </li>
<li> <a href="#RNA">RNA-seq</a> </li>
<li> <a href="#miRNA">miRNA-seq</a> </li>
<li> <a href="#ChIP">ChIP-, DNase-, and Methyl-seq</a> </li>
<li> <a href="#CNA">CNA-seq</a> </li>
<li> <a href="#meta">Metagenomics</a> </li>
</ol>
<hr>
<ul>
<b><a name="quality">Quality control</a></b>
<li> <a href="fastqc.html">Read quality with FastQC</a></li>
<li> <a href="fastx-statistics.html">Quality statistics with FASTX</a></li>
<li> <a href="prinseq-statistics.html">Read quality statistics with PRINSEQ </a> </li>
<li> <a href="rseqc.html">RNA-seq quality metrics with RseQC</a></li>
<li> <a href="deseq2-pca-heatmap.html">PCA and heatmap of samples with DESeq2</a></li>
<br>
<br>
<b><a name="preprocessing">Preprocessing</a></b>
<li> <a href="trimmomatic.html">Trim reads with Trimmomatic</a></li>
<li> <a href="prinseq-trimmer.html">Trim reads for several criteria with PRINSEQ </a> </li>
<li> <a href="fastx-trimmer.html">Trim reads with FASTX</a> </li>
<li> <a href="tagcleaner-trim.html">Trim primers/adaptors with TagCleaner</a></li>
<li> <a href="tagcleaner-predict.html">Predict primers/adaptors with TagCleaner</a></li>
<li> <a href="tagcleaner-statistics.html">Statistics for primers/adaptors with TagCleaner</a></li>
<li> <a href="prinseq-filter.html">Filter reads for several criteria with PRINSEQ</a> </li>
<li> <a href="fastx-quality-filter.html">Filter reads for quality with FASTX</a> </li>
<li> <a href="fastx-clipper.html">Filter reads for adapters, length and Ns with FASTX</a></li>
<br>
<br>
<b><a name="utilities">Utilities</a></b>
<li> <a href="ngs-create-experiment.html">Define NGS experiment </a> </li>
<li> <a href="ngs-filter-annotations.html">Filter by column term </a> </li>
<li> <a href="ngs-filter-results-column.html">Filter by column value </a> </li>
<li> <a href="extract-samples-from-dataset.html">Extract samples from dataset </a> </li>
<li> <a href="process-preprocessed-counts.html">Preprocess count table </a> </li>
<li> <a href="fastx-renamer.html">Rename reads</a> </li>
<li> <a href="samtools-rmdup.html">Remove duplicate reads from BAM </a> </li>
<li> <a href="samtools-index.html">Index BAM </a> </li>
<li> <a href="samtools-sort-index-BAM.html">Sort and index BAM</a> </li>
<li> <a href="samtools-convert-SAMtoBAM-sort-index.html">Convert SAM to BAM, sort and index</a> </li>
<li> <a href="bedtools-bamtobed.html">Convert BAM to BED </a> </li>
<li> <a href="fastx-fastq-to-fasta.html">Convert FASTQ to FASTA</a> </li>
<li> <a href="samtools-merge.html">Merge BAM </a> </li>
<li> <a href="samtools-idxstats.html">Statistics for BAM </a> </li>
<li> <a href="samtools-subset.html">Make a subset of BAM  </a> </li>
<li> <a href="samtools-count.html">Count alignments in BAM  </a> </li>
<li> <a href="samtools-consensus.html">Create consensus sequence from BAM </a> </li>
<li> <a href="unique-alignments-from-bam.html"> Retrieve unique alignments from BAM</a></li>
<li> <a href="bedtools-sort.html">Sort BED </a> </li>
<li> <a href="sort-gtf.html">Sort GTF</a></li>
<li> <a href="sort-vcf.html">Sort VCF</a></li>
<li> <a href="bedtools-fastafrombed.html">FASTA from BED </a> </li>
<li> <a href="select_columns.html">Table converter</a></li>
<li> Extract features from BED </li>
<br>
<br>
<b><a name="regions">Matching genomic regions</a></b>
<li> <a href="FindOverlappingTool.html">Find overlapping regions </a> </li>
<li> <a href="RemoveOverlappingTool.html">Remove overlapping regions </a> </li>
<li> <a href="CombineRegionsTool.html">Combine region files </a> </li>
<li> <a href="bedtools-subtractbed.html">Subtract BED </a> </li>
<li> <a href="bedtools-intersectbed.html">Intersect BED </a> </li>
<li> <a href="bedtools-closestbed.html">Closest BED </a> </li>
<li> <a href="bedtools-windowbed.html">Window BED </a> </li>
<li> <a href="bedtools-mergebed.html">Merge BED </a> </li>
<li> <a href="bedtools-coveragebed.html">Coverage BED </a> </li>
<li> <a href="bedtools-genomecoveragebed.html">Genome coverage BED </a> </li>
<li> <a href="bedtools-overlap.html">Overlap BED </a> </li><commit_msg>Updated tool list.<commit_after><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html lang="en">
<head><title>Chipster manual</title></head>
<body>

<h2>Analysis tools for next generation sequencing data</h2>
			

<p>Chipster's NGS analysis tools are grouped in the categories listed below. Chipster also contains a <a href="genomeBrowser.html">built-in genome browser</a>,
allowing you to view reads and results in their genomic context.</p>

<ol>
<li> <a href="#quality">Quality control</a> </li>
<li> <a href="#preprocessing">Preprocessing</a> </li>
<li> <a href="#utilities">Utilities</a> </li>
<li> <a href="#regions">Matching genomic regions</a> </li>
<li> <a href="#alignment">Alignment</a> </li>
<li> <a href="#variants">Variants</a> </li>
<li> <a href="#RNA">RNA-seq</a> </li>
<li> <a href="#miRNA">miRNA-seq</a> </li>
<li> <a href="#ChIP">ChIP-, DNase-, and Methyl-seq</a> </li>
<li> <a href="#CNA">CNA-seq</a> </li>
<li> <a href="#meta">Metagenomics</a> </li>
</ol>
<hr>
<ul>
<b><a name="quality">Quality control</a></b>
<li> <a href="fastqc.html">Read quality with FastQC</a></li>
<li> <a href="fastx-statistics.html">Quality statistics with FASTX</a></li>
<li> <a href="prinseq-statistics.html">Read quality statistics with PRINSEQ </a> </li>
<li> <a href="rseqc.html">RNA-seq quality metrics with RseQC</a></li>
<li> <a href="deseq2-pca-heatmap.html">PCA and heatmap of samples with DESeq2</a></li>
<br>
<br>
<b><a name="preprocessing">Preprocessing</a></b>
<li> <a href="trimmomatic.html">Trim reads with Trimmomatic</a></li>
<li> <a href="prinseq-trimmer.html">Trim reads for several criteria with PRINSEQ </a> </li>
<li> <a href="fastx-trimmer.html">Trim reads with FASTX</a> </li>
<li> <a href="tagcleaner-trim.html">Trim primers/adaptors with TagCleaner</a></li>
<li> <a href="tagcleaner-predict.html">Predict primers/adaptors with TagCleaner</a></li>
<li> <a href="tagcleaner-statistics.html">Statistics for primers/adaptors with TagCleaner</a></li>
<li> <a href="prinseq-filter.html">Filter reads for several criteria with PRINSEQ</a> </li>
<li> <a href="fastx-quality-filter.html">Filter reads for quality with FASTX</a> </li>
<li> <a href="fastx-clipper.html">Filter reads for adapters, length and Ns with FASTX</a></li>
<br>
<br>
<b><a name="utilities">Utilities</a></b>
<li> <a href="ngs-create-experiment.html">Define NGS experiment </a> </li>
<li> <a href="ngs-filter-annotations.html">Filter table by column term </a> </li>
<li> <a href="ngs-filter-results-column.html">Filter table by column value </a> </li>
<li> <a href="filter-bed-value.html">Filter BED by column value </a> </li>
<li> <a href="extract-samples-from-dataset.html">Extract samples from table </a> </li>
<li> <a href="select_columns.html">Table converter</a></li>
<li> <a href="sort_and_select_columns.html">Sort table by column</a></li>
<li> <a href="join_tsv_files.html">Join tables</a></li>
<li> <a href="process-preprocessed-counts.html">Preprocess count table </a> </li>
<li> <a href="normalise-counts.html">Normalize count table </a> </li>
<li> <a href="annotate-ensembl-ids.html">Annotate Ensembl identifiers </a> </li>
<li> <a href="deseq2-normalized-counts-for-gene.html">Plot normalized counts for a gene</a> </li>
<li> <a href="a5-miseq.html">A5 assembly pipeline for microbial genomes</a> </li>
<li> <a href="samtools-index.html">Index BAM </a> </li>
<li> <a href="samtools-sort-index-BAM.html">Sort and index BAM</a> </li>
<li> <a href="samtools-convert-SAMtoBAM-sort-index.html">Convert SAM to BAM, sort and index</a> </li>
<li> <a href="samtools-subset.html">Make a subset of BAM  </a> </li>
<li> <a href="samtools-merge.html">Merge BAM </a> </li>
<li> <a href="samtools-idxstats.html">Statistics for BAM </a> </li>
<li> <a href="samtools-count.html">Count alignments in BAM  </a> </li>
<li> <a href="samtools-rmdup.html">Remove duplicate reads from BAM </a> </li>
<li> <a href="samtools-consensus.html">Create consensus sequence from BAM </a> </li>
<li> <a href="unique-alignments-from-bam.html"> Retrieve unique alignments from BAM</a></li>
<li> <a href="bedtools-bamtobed.html">Convert BAM to BED </a> </li>
<li> <a href="fastx-fastq-to-fasta.html">Convert FASTQ to FASTA</a> </li>
<li> <a href="samtools-index-fasta.html">Index FASTA</a> </li>
<li> <a href="subset-fastq.html">Make a subset of FASTQ</a> </li>
<li> <a href="fastx-renamer.html">Rename reads in FASTQ</a> </li>
<li> <a href="fastx-collapser.html">Remove duplicate reads from FASTQ</a> </li>
<li> <a href="bedtools-sort.html">Sort BED </a> </li>
<li> <a href="sort-gtf.html">Sort GTF</a></li>
<li> <a href="sort-vcf.html">Sort VCF</a></li>
<li> <a href="sort-tsv.html">Sort TSV</a></li>
<li> <a href="bedtools-fastafrombed.html">FASTA from BED </a> </li>
<li> <a href="extract-features-from-BED.html">Extract features from BED </a> </li>
<li> <a href="DownloadFile.html">Download file from url to server</a></li>
<li> <a href="srafetch.html">Retrieve FASTQ files from SRA database</a></li>
<li> <a href="srabamfetch.html">Retrieve BAM files from SRA database</a></li>
<li> <a href="ensemblfetch.html">Retrieve sequences for a given organism in Ensembl</a></li>
<li> <a href="gunzip.html">Extract .gzip file</a></li>
<li> <a href="extract_gzip_tar.html">Extract .gzip.tar file</a></li>
<br>
<br>
<b><a name="regions">Matching genomic regions</a></b>
<li> <a href="FindOverlappingTool.html">Find overlapping regions </a> </li>
<li> <a href="RemoveOverlappingTool.html">Remove overlapping regions </a> </li>
<li> <a href="CombineRegionsTool.html">Combine region files </a> </li>
<li> <a href="bedtools-subtractbed.html">Subtract BED </a> </li>
<li> <a href="bedtools-intersectbed.html">Intersect BED </a> </li>
<li> <a href="bedtools-closestbed.html">Closest BED </a> </li>
<li> <a href="bedtools-windowbed.html">Window BED </a> </li>
<li> <a href="bedtools-mergebed.html">Merge BED </a> </li>
<li> <a href="bedtools-coveragebed.html">Coverage BED </a> </li>
<li> <a href="bedtools-genomecoveragebed.html">Genome coverage BED </a> </li>
<li> <a href="bedtools-overlap.html">Overlap BED </a> </li>
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