Error Locating Program Bowtie-inspect
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Tophat Paired End Example
papori Bioinformatics 8 09-03-2014 02:16 PM bowtie index problem (bowtie-build and then bowtie-inspect) tgenahmet Bioinformatics 4 09-10-2013 11:51 AM tophat command line Cufflinks - 'u' Class Code - Consistently Returned AndrewCarpenter Bioinformatics 3 01-19-2011 06:16 PM bowtie-inspect question dicty Bioinformatics 0 12-02-2010 04:45 PM help with bowtie-inspect nimmi RNA Sequencing 0 10-25-2010 11:28 AM tophat2 tutorial Thread Tools 11-12-2010, 10:27 AM #1 pettervikman Member Location: Sweden Join Date: Nov 2009 Posts: 23 Bow-tie inspect returned an error Hi all I'm trying to run TopHat for the first time. I've checked the installation with the complementary test data set and that worked. Now with my own data set I get that message right after it tries to create the
Tophat Tutorial
rat rn4.fa file since it's lacking in the index_folder. I've downloaded and unpacked the files from the bowtie/tophat webpage and I ran the make script. I've asked our IT people but since they are even more unfamiliar then me (which says a lot) with this program I got no help. So any help would be greatly appreciated! I 've pasted the entire message from TopHat below. Sincerely /Petter [1] 19633 [[emailprotected] BaseCalls]$ [Fri Nov 12 19:28:30 2010] Beginning TopHat run (v1.1.2) ----------------------------------------------- [Fri Nov 12 19:28:30 2010] Preparing output location ./tophat_out/ [Fri Nov 12 19:28:30 2010] Checking for Bowtie index files Error: Could not find Bowtie index files /data/archive/bowtie-indexes/chr*.* tophat -r 100 -p 4 --library-type fr-unstranded chr s_1_1_* s_1_2_* & [2] 19634 [1] Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded chr* s_1_1_* s_1_2_* [[emailprotected] BaseCalls]$ [Fri Nov 12 19:28:40 2010] Beginning TopHat run (v1.1.2) ----------------------------------------------- [Fri Nov 12 19:28:40 2010] Preparing output location ./tophat_out/ [Fri Nov 12 19:28:40 2010] Checking for Bowtie index files Error: Could not find Bowtie index files /data/archive/bowtie-indexes/chr.* tophat -r 100 -p 4 --library-type fr-unstranded rn4 s_1_1_* s_1_2_* & [3] 19635 [2] Exit 1 tophat -r 1
and comments about TopHat can be posted on the Tuxedo Tools Users Google Group. Please use tophat.cufflinks@gmail.com for private communications only. Please do not email technical questions to TopHat tophat2 download contributors directly. Releases version 2.1.1 2/23/2016 Source code Linux x86_64 binary Mac OS bowtie2 index X x86_64 binary Related Tools Cufflinks: Isoform assembly and quantitation for RNA-Seq Bowtie: Ultrafast short read alignment TopHat-Fusion: An algorithm
Bowtie Index
for Discovery of Novel Fusion Transcripts CummeRbund: Visualization of RNA-Seq differential analysis Publications Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics doi:10.1093/bioinformatics/btp120 Langmead B, Trapnell C, Pop http://seqanswers.com/forums/showthread.php?t=7824 M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. Kim D and Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biology 2011, 12:R72 Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. . Genome Biology 2013, https://ccb.jhu.edu/software/tophat/tutorial.shtml 14:R36 Contributors Cole Trapnell Daehwan Kim Geo Pertea Harold Pimentel Ryan Kelley Lior Pachter Steven Salzberg Links Center for Computational Biology at Johns Hopkins University Genome Sciences Department at University of Washington University of Maryland University of California, Berkeley UMD CBCB UMD Computer Science Berkeley Mathematics UMIACS Getting started Install quick-start Test the installation Preparing your reference Preparing your reads Running TopHat Examining your results Install quick-start Download and extract the latest Bowtie 2 (or Bowtie) releases. Note that you can use either Bowtie 2 (the default) or Bowtie (--bowtie1) and you will need the following Bowtie 2 (or Bowtie) programs in your PATH: bowtie2 (or bowtie) bowtie2-build (or bowtie-build) bowtie2-inspect (or bowtie-inspect) Installing a pre-compiled binary release In order to make it easy to install TopHat we provide a few binary packages to save users from the occasionally frustrating process of building TopHat themselves, which requires a certain development environment and the Boost libraries installed. To use the binary packages, simply download the appropriate one for your platform, unpack it, and make sure the TopHat binaries are in a directory in your PATH environment variable (or create a symbolic link to the included tophat2 scrip
[ date ] [ thread ] [ subject ] [ author ] Looks like the "development" package for zlib is missing. Rather than https://lists.galaxyproject.org/pipermail/galaxy-dev/2011-August/006259.html building SAMtools from source, you may want to check if there is a packaged version for your Linux distribution. The package manager [apt-get on Ubuntu(?); I'm on CentOS http://bowtie-bio.sourceforge.net/manual.shtml and use yum] should handle bringing in any dependencies if they are not already installed. If you do indeed want to build from source, use your package manager error locating to install the needed dependency, typically something like zlib-devel. -- Olen On Mon, Aug 1, 2011 at 13:53, Luciano Cosme
memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. For release updates, subscribe to the mailing list. Links Bowtie GitHub repository Report an issue Bowtie Mailing list Related Tools Bowtie 2: Fast, accurate read alignment Crossbow: Genotyping, cloud computing Tophat: RNA-Seq splice junction mapper Cufflinks: Isoform assembly, quantitation Myrna: Cloud, differential gene expression Lighter: Fast error correction Other tools using Bowtie Pre-built indexes Consider using Illumina's iGenomes collection. Each iGenomes archive contains pre-built Bowtie and Bowtie 2 indexes. H. sapiens, NCBI GRCh38 2.7 GB H. sapiens, UCSC hg19 2.7 GB or: part 1 - 1.7 GB, part 2 - 1.0 GB colorspace: full, or part 1, part 2 H. sapiens, UCSC hg18 2.7 GB or: part 1 - 1.7 GB, part 2 - 1.0 GB colorspace: full, or part 1, part 2 H. sapiens, NCBI v37 2.7 GB or: part 1 - 1.7 GB, part 2 - 1.0 GB colorspace: full, or part 1, part 2 H. sapiens, NCBI v36 2.7 GB or: part 1 - 1.7 GB, part 2 - 1.0 GB colorspace: full, or part 1, part 2 M. musculus, UCSC mm8 2.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 M. musculus, UCSC mm9 2.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 M. musculus, NCBI v37 2.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 R. norvegicus, UCSC rn4 2.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 B. taurus, UMD v3.0 2.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 C. familiaris, UCSC canFam2 2.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 G. gallus, UCSC, galGal3 1.1 GB colorspace: full D. melanogaster, Flybase, r5.22 150 MB colorspace: full A. thaliana, TAIR, TAIR9 120 MB colorspace: full C. elegans, Wormbase, WS200