we have set up a Galaxy server for internal use. We would like to provide indexes for NGS mapping tools for a set of organisms that are relevant to our research. While bowtie has a repository of such indexes, other tools, e.g. bwa, don't seem to have one, so we have to build our own. Is there a repository of pre-built indexes for all mapping tools supported by Galaxy somewhere?
Yury V. Bukhman, Ph.D.
Associate Scientist, Bioinformatics
Great Lakes Bioenergy Research Center
University of Wisconsin - Madison
445 Henry Mall, Rm. 513
Madison, WI 53706, USA
Phone: 608-890-2680 Fax: 608-890-2427
Dan Blankenberg will be giving two workshops on Galaxy at the University of
Pittsburgh on April 6. The presentations are open to the public. See below
for details and please contact Dan, or Carrie Iwema at Pitt, if you have any
Intro to Galaxy
Dan Blankenberg, PhD
Center for Comparative Genomics & Bioinformatics
Penn State University
Galaxy allows you to do analyses you cannot do anywhere else without the
need to install or download anything.
You can analyze multiple alignments, compare genomic annotations, profile
metagenomic samples & more...
Wednesday 6th April
*10 am – 12 pm Intro to Galaxy (general interest)
*2 pm - 4 pm Working w/NGS Data (advanced users)
University of Pittsburgh
Conference Room B
You are welcome to bring your laptop.
Carrie L. Iwema, PhD, MLS
Information Specialist in Molecular Biology
Health Sciences Library System
University of Pittsburgh
200 Scaife Hall
3550 Terrace St
Pittsburgh, PA 15261
Is there a way to unsubscribe from Galaxy e-mail list?
Please, let me know.
Massimo Bionaz PhD
Institute for Genomic Biology,
University of Illinois
366 Animal Sciences Laboratory
1207 W. Gregory Dr.
Urbana, IL 61801
Office Tel: 1-217-333-6189
If Cufflinks works without a reference GTF, then the problem is the mismatch b/t your GTF and your bam file. A couple things to check:
(1) that your genome chrom names in F3.csfata match those in your GTF; if not, you'll need to modify your GTF to match the names in your fasta.
(2) that your GTF is sorted as your BAM is sorted.
If these issues don't solve your problem, it's best to use the Cufflinks help email that I noted in my previous email.
On Mar 31, 2011, at 10:32 AM, lishiyong wrote:
> Hello,I don't use Galaxy.But I have uploaded the file(sorted file 20:test_44.bam refgene.gtf : ) It's works OK without the reference GTF file ,while with reference, I can't gain the right results, I do these in my computer.
> 发件人： Jeremy Goecks
> 发送时间： 2011-03-31 21:36:52
> 收件人： lishiyong
> 抄送： galaxy-user
> 主题： Re: [galaxy-user] cufflinks FPKM
> It's not clear whether you're using Galaxy. If you're using Galaxy, please share you history with me (History Options --> Share/Publish --> Share with User --> my email) and I'll take a look; otherwise, Cufflinks has an email list for questions: tophat.cufflinks(a)gmail.com
> On Mar 31, 2011, at 3:39 AM, lishiyong wrote:
>> I gain the SOLiD sequencing data.I used bowtie to map human genome then I sort the sam file .I used cuffinks to calculate FPKM with the sam file ,human gtf file .it gives 0 FPKM values and this is for all genes .what's the reason?
>> (1) bowtie -C human_hg18_color -f F3.csfasta -Q F3_QV.qual -v 2 -k 100 -p 6 --mapq --sam test.sam
>> (2) samtools view -uS test.sam 2>/dev/null | samtools sort -m 2000000000 - test.bam
>> (3) cufflinks -G refGene_hg18.gtf test.bam.bam
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org. Please keep all replies on the list by
>> using "reply all" in your mail client. For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
I gain the SOLiD sequencing data.I used bowtie to map human genome then I sort the sam file .I used cuffinks to calculate FPKM with the sam file ,human gtf file .it gives 0 FPKM values and this is for all genes .what's the reason?
(1) bowtie -C human_hg18_color -f F3.csfasta -Q F3_QV.qual -v 2 -k 100 -p 6 --mapq --sam test.sam
(2) samtools view -uS test.sam 2>/dev/null | samtools sort -m 2000000000 - test.bam
(3) cufflinks -G refGene_hg18.gtf test.bam.bam
My IT people are setting us up for an instantiation of Galaxy on campus for my course and
faculty to use. They have most everything working on our server but when I get to the
Megablast there are no databases. I need to give them the instructions for how to set up for
databases like NR and maybe the human HGTS. Where can I find that information to give to
the people that will understand it?
Douglas Rhoads, Professor of Biological Sciences
Director of Graduate Program in Cell and Molecular Biology
601 SCEN, Dept. of Biological Sciences,
1 University of Arkansas, Fayetteville, AR 72701
phone: 479-575-3251 FAX: 479-575-4010
I already analysed some of our data with your framework and I want to thank
you for your great work. But lately I stumbled on some strange behavior - I
used the "aaChanges"-tool, as well as the Gene "BED-to-Codon"-tool with the
same Gene-BED-File and compared the results. What I did:
chr17 3763624 3794037 uc002fwt.2 0 - 3765504 3788981 0
#example-output of "aaChanges"
chr17 3775847 3775848 C uc002fwt.2 Glu:Gly 375 T
#example-output of "BED-to-Codon"
chr17 3773172 3773175 uc002fwt.2 0 -
chr17 3773175 3773178 uc002fwt.2 0 -
chr17 3773178 3773181 uc002fwt.2 0 -
chr17 3775849 3775852 uc002fwt.2 0 -
chr17 3775852 3775855 uc002fwt.2 0 -
Comparing both results, the "BED-to-Codon" actually presents no codon at
position 3775848 - here the fist codon is starting at 3775849. But in fact,
looking at the ucsc browser, "aaChanges" is right. There are another few
examples (~5/1500 snps) and apparently most of them are positions among the
first codon in an exon.
Did anyone meet this problem before? What is my mistake?