https://gcat.davidson.edu/GcatWiki/api.php?action=feedcontributions&feedformat=atom&user=Vifang 2026-05-18T12:18:37Z User contributions MediaWiki 1.28.2 https://gcat.davidson.edu/GcatWiki/index.php?title=How_does_it_compare_to_HTSeq%3F&diff=19136 2018-02-06T15:02:44Z

<p>Vifang: Created page with &quot;A Python library to facilitate the rapid development of such scripts. HTSeq offers...classes to represent data, such as genomic coordinates, sequences, sequencing reads, align...&quot;</p> <hr /> <div>A Python library to facilitate the rapid development of such scripts. HTSeq offers...classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. The researchers also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes (Source: http://www.rna-seqblog.com/htseq-a-python-framework-to-work-with-high-throughput-sequencing-data/)</div>

Vifang https://gcat.davidson.edu/GcatWiki/index.php?title=What_does_Cufflinks_do%3F&diff=19128 2018-02-06T14:56:05Z

<p>Vifang: Created page with &quot;This tool takes TopHat-processed short reads and assembles them into as many mRNA transcripts as it can, and as complete as possible; then Cufflinks measures the abundance of...&quot;</p> <hr /> <div>This tool takes TopHat-processed short reads and assembles them into as many mRNA transcripts as it can, and as complete as possible; then Cufflinks measures the abundance of each transcript (Source: MiniMouse tutorial)<br /> <br /> Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols (Source https://ngs.csr.uky.edu/Cufflinks)<br /> <br /> *note to self: TopHat takes RNA-seq data and compares to known genome, Cufflink assembles the data and tells us how much of it there is --&gt; greater abundance = greater expression</div>

Vifang https://gcat.davidson.edu/GcatWiki/index.php?title=Owen_and_Vivienne&diff=19123 2018-02-06T14:44:39Z

<p>Vifang: </p> <hr /> <div>[[What does Cufflinks do?]]<br /> <br /> [[How does it compare to HTSeq?]]</div>

Vifang https://gcat.davidson.edu/GcatWiki/index.php?title=Owen_and_Vivienne&diff=19122 2018-02-06T14:44:26Z

<p>Vifang: </p> <hr /> <div>[[What does Cufflinks do?]]<br /> <br /> How does it compare to HTSeq?</div>

Vifang https://gcat.davidson.edu/GcatWiki/index.php?title=Owen_and_Vivienne&diff=19121 2018-02-06T14:43:38Z

<p>Vifang: </p> <hr /> <div>[What does Cufflinks do? <br /> ]<br /> <br /> How does it compare to HTSeq?</div>

Vifang