The data comes from a variety of ... First of all, ... Alternatively, you can add packages I listed in my last email to the list of packages under _required_packages method. With this function, I can drag _multiple_ small files (for example,'bed' files) in the special region of the page, which is easy to use. 3.Start automatically when uploading finished Some large
Hence just curious what a smoother solution would be. > > > In general - is the cloud install using the mi- script to install the tools? However, when it comes to R and rpy, those tools are (as you discovered) not being installed via those scripts; they are installed from packages but, in the case of Galaxy We need to wait until the uploading is done because we cannot assign a task to an unfinished uploading file. I prepared the reference index fi... .gtf file error in Tophat2 - Error at parsing .tlst line (invalid strand): I'm trying to align my reads to a genome + transcriptome, which
if I run tophat on this some.fastq file > @Read_num:9:trans:"ENST00000618181":start:935873:ex... Tophat Error When "Reporting Output Tracks" I'm learning tophat . I need to convert a ... [Errno 8] Exec Format Error Using Tophat 1.3.1 Hi all, I've installed Tophat 1.3.1 following these instructions and when I run the test comma...
GBiz is too! Latest News Stories: Docker 1.0Heartbleed Redux: Another Gaping Wound in Web Encryption UncoveredThe Next Circle of Hell: Unpatchable SystemsGit 2.0.0 ReleasedThe Linux Foundation Announces Core Infrastructure in tophat command, you need to use your fasta (genome file) and RNAseq files (R1 and R2). Thank you.Luciano ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the But maybe it's not so hard for displaying the _current percent_ of uploading, it's really helpful and comfortable for users (_a countdown timer_ will be better). 2.
The wiki page on dependencies > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies > correctly links to the R project as http://www.r-project.org/ > > you are correct, however the tools_fabfile.py has > > version = "2.11.1" Galaxy Samtools To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Thread at a glance: Previous Message by Date: Re: [galaxy-dev] [galaxy-user] mi-tools- tools_fabfile.py permissions requirements Tophat2 : Error: Segment-Based Junction Search Failed With Err =-11 Hi, I tried yesterday tophat 2.0.4 with fusion-search on several on my samples and I have an err... ADD REPLY • link written 5.2 years ago by Ning-Yi Shao • 330 0 5.3 years ago by Ido Tamir ♦ 4.6k Austria Ido Tamir ♦ 4.6k wrote: As others posted
Tophat syntax to align query sequences to reference index Dear all, I need to align some fastq files to the human genome. Run tophat command. These are the steps I followed for processing... Problem with TopHat in Galaxy using data from Nature Protocols Hi, I am a graduate student who began RNA-seq data analysis recently.
bgzf.c -o bgzf.oIn file included from bgzf.c:36:0:bgzf.h:30:18: fatal error: zlib.h: No such file or directory compilation terminated.Hi,From the above lines error message it is clear that zlib.h is not installed in https://www.biostars.org/p/10249/ here is the Makefile I'm using: include tools.mk REF=./chr22 REF.bowtie=$(... Error Locating Program Samtools Can anyone help? [Wed Aug 17 19:41:10 2011] Beginning TopHat run (v1.3.1) ----------------------------------------------- [Wed Aug 17 19:41:10 2011] Preparing output location /d/RNAseq/Tophat/ [Wed Aug 17 19:41:10 2011] Checking for Bowtie index bgzf.c -o bgzf.o > In file included from bgzf.c:36:0: > bgzf.h:30:18: fatal error: zlib.h: No such file or directory > compilation terminated. > make: *** [bgzf.o] Error 1 > make: Leaving
try to put the full path to the tophat executable in the exec command. Tophat Error: Segment-Based Junction Search Failed With Err Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this er... Why its *.gtf ? To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___________________________________________________________ Please keep all replies on the list by using
Enis On Mon, Aug 1, 2011 at 12:49 PM, Joseph Hargitai
I'm trying to run tophat for rna-seq analysis. Tophat2 index problem I'm trying to align RNA-seq data of wheat genome so i used bowtie2 with large index option to bui... error: segment-based junction search failed with err =-5 Reason: image not found tophat2 mapping error I always use this command and mapping is successfully end. I'm trying to run tophat for rna-seq analysis.
part? http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup For next time, the [email protected] mailing list would be the best place to send new questions or even follow-up questions to this one if problems persist. Contact Us - SEQanswers Home - Archive - Top Powered by vBulletin Version 3.8.9Copyright ©2000 - 2016, vBulletin Solutions, Inc. or you can export your tophat path into PATH Check this post http://seqanswers.com/forums/showthread.php?t=12688 Last edited by chenyao; 08-17-2011 at 04:37 AM.
If you would like to follow suit and install those tools from packages, these are the ones (for debian):r-base, r-base-core, r-base-core-ra, r-base-dev, r-base-html, python-rpy As far as the permissions issues goes, Best Wishes, Hanfei Sun ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. Password Register FAQ Community Calendar Today's Posts Search You are currently viewing the SEQanswers forums as a guest, which limits your access. I can imagine a story like this: I am quite tired after a whole day's busy work, but some sequencing data still need to be analyzed because I will show it
bgzf.c -o bgzf.oIn file included from bgzf.c:36:0:bgzf.h:30:18: fatal error: zlib.h: No such file or directory compilation terminated.make: *** [bgzf.o] Error 1make: Leaving directory `/home/koala2/Desktop/galaxy/samtools'make: *** [lib-recur] Error 1make: Leaving directory `/home/koala2/Desktop/galaxy/samtools' Tophat Error Hello, I was trying to run tophat v1.3.2 on SOLID data and I have this erro... I've been trying to find my answer via Google but came up empty handed. But if i copy the command into the shell it works fine...so what is wrong?!
If you would like to, please add in your ideas as enhancement requests to our public ticket system at: http://bitbucket.org/galaxy/galaxy-central/issues Take care, Jen Galaxy team On 7/28/11 11:45 AM, å çè Thank you.Luciano ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the TopHat: Error: Couldn't build bowtie index with err = 1 Hi I'm trying to run TopHat on a Cloudman Galaxy instance and I keep getting the below error. I'm new to scripting,...
However RNA-STAR is way faster than tophat and bowtie. ADD COMMENT • link modified 18 months ago • written 18 months ago by Parham • 1.2k 0 18 months ago by amnoronha1016 • Click here to register now, and join the discussion Community Links Members List Search Forums Show Threads Show Posts Tag Search Advanced Search Go to Page... just leave in your directory. Could anybody help?