BHSC_Bioinformatics/formats.html at master · deannachurch/BHSC_Bioinformatics · GitHub

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        <div id="header"><h1>Bar Harbor Short Course on Medical and Experimental Mammalian Genetics</h1></div>
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            <div id="sidebar"><h4>Pages</h4>
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                <li><a href="../index.html">Home</a></li>
                <li><a href="../2014_07_21">Day 1</a></li>
                <li><a href="../2014_07_23">Day 2</a></li>
                <li><a href="../2014_07_24">Day 3</a></li>
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                <li><a href="../2014_07_29">Day 5</a></li>
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                <li><a href="formats.html">File Formats</a></li>
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                <legend>File formats</legend>
                <p class="subtitle">Defined file formats used by the bioinformatics community. If you are using new data or trying to use new viewers, it is important to note what formats are supported. <span class="strong">Note</span>: while many of these formats have specified usage, there can many variants of these files in circulation and these variants may cause some readers to break. </p>
                <p>Note: Formats that are 0-based start counting the first base as 0, while formats that are 1-based start counting the first base at 1. It is important to know whether you are using a 0-based or 1-based system!</p>
                <p><span class="strong">SAM/BAM</span>(<a href="http://samtools.sourceforge.net/SAM1.pdf">http://samtools.sourceforge.net/SAM1.pdf</a>): SAM is a tab-delimited file format for expressing sequence alignment and mapping. BAM is the binary form of SAM. (1-based)</p>
                <p><span class="strong">BED</span> (<a href="http://genome.ucsc.edu/FAQ/FAQformat.html#format1">http://genome.ucsc.edu/FAQ/FAQformat.html#format1</a>): A generic format typically used to define genomic intervals and describe how these intervals should be rendered in the UCSC browser. (0-based)</p>
                <p><span class="strong">bigBed</span> (<a href="http://genome.ucsc.edu/FAQ/FAQformat.html#format1.5">http://genome.ucsc.edu/FAQ/FAQformat.html#format1.5</a>): a binary transformation of BED that allows for larger datasets to be transferred and displayed more quickly. (0-based)</p>
                <p><span class="strong">GFF</span> (<a href="http://www.sanger.ac.uk/resources/software/gff/">http://www.sanger.ac.uk/resources/software/gff/</a>): a format that was defined for describing gene annotation. (1-based) </p>
                <p><span class="strong">GTF</span> (<a href="http://mblab.wustl.edu/GTF2.html">http://mblab.wustl.edu/GTF2.html</a>): a refinement of GFF  that tries to tighten the specification. (1-based)</p>
                <p><span class="strong">GFF3</span> (<a href="http://www.sequenceontology.org/gff3.shtml">http://www.sequenceontology.org/gff3.shtml</a>): another attemp to extend GFF and harden the definition. (1-based)</p>
                <p><span class="strong">GVF</span> (<a href="http://www.sequenceontology.org/resources/gvf.html">http://www.sequenceontology.org/resources/gvf.html</a>): A GFF3 like format that is specific for describing variation. (1-based)</p>
                <p><span class="strong">VCF</span> (<a href="http://www.1000genomes.org/node/101">http://www.1000genomes.org/node/101</a>): Variant call format, developed by the 1000 genomes project to handle both variant defintion and genotype information. (1-based, but uses 0 or N+1 to denote the telomere)</p>
                <p><span class="strong">HGVS</span> (<a href="http://www.hgvs.org/mutnomen">http://www.hgvs.org/mutnomen</a>): A reporting format for the description of sequence variants.</p>
                <p><span class="strong">MAF</span> (<a href="http://genome.ucsc.edu/FAQ/FAQformat.html#format5">http://genome.ucsc.edu/FAQ/FAQformat.html#format5</a>): Multiple alignment format. (0-based)</p>
                <p><span class="strong">WIG</span> (<a href="http://genome.ucsc.edu/goldenPath/help/wiggle.html">http://genome.ucsc.edu/goldenPath/help/wiggle.html</a>): format for continuous data (like gc percent). (1-based)</p>
                <p><span class="strong">FASTQ</span> (<a href="http://maq.sourceforge.net/fastq.shtml">http://maq.sourceforge.net/fastq.shtml</a>): A format used for storing the bases and quality scores for a sequence read; used by many tools for analyzing next generation sequence.</p>
                <p><span class="strong">FASTA</span> (<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml">http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml</a>): common format for storing sequence data that is used by many tools.</p>
                <p><a href="https://main.g2.bx.psu.edu/" title="Galaxy">Galaxy</a> has tools that help you convert one format to another.</p>
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