http://ccb.jhu.edu/software/tophat/index.shtml http://cole-trapnell-lab.github.io/cufflinks/tools/

Building Bowtie index failure (tophat2, bowtie2) - Stack Overflow

WebTopHat is an open-source bioinformatics tool for the throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies (e.g. RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. [1] TopHat aligns RNA-Seq reads to mammalian-sized genomes. http://ccb.jhu.edu/software/tophat/faq.shtml smooth black

Tophat can

Webtophat Link to section 'Introduction' of 'tophat' Introduction TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. WebBow Tie Hat - Etsy. Check out our bow tie hat selection for the very best in unique or custom, handmade pieces from our bow ties shops. Etsy. Search for items or shops. WebYou can use Bowtie 2 to align reads of about 50 to 100s or 1,000s of characters. For human genome, the memory footprint is approximately 3.2 GB. Bowtie 2 forms the basis for other tools like Tophat, a fast splice junction mapper for RNA-seq reads, and Cufflinks, a tool for transcriptome assembly and isoform quantitation from RNA-seq reads. smooth black crystal