[galaxy-user] how to use user-defined reference?

Hi everyone, I am wondering if I can use user-defined reference instead of selecting the reference genome listed in Galaxy while doing mapping. If we can, how can I choose the uploaded reference instead of selecting the reference genome? Any ideas are greatly appreciated! Cheers, Yan

[galaxy-user] Job is waiting to run

Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). I was trying to upload two files (one is 1.6G and the other is 1.9G) but it was labeled as Job is waiting to run forever. Could you please let me know the possible reasons? Sincerely, Yan

[galaxy-user] FTP upload problem

Hi everyone, When I tried to upload my files using Filezilla, I got the error message 530 Sorry, the maximum number of clients (3) for this user are already connected. Can anyone give me some suggestions how to solve this problem? I have been stuck here for a whole day. Thanks very much!

[galaxy-user] Cuffdiff errors

Hello, I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 samples (A and B). I did Cufflinks and Cuffmerge before running Cuffdiff. I ran Cuffdiff with the following options: Cuffmerge + Bowtie A, B (sorted required by Cufflinks after mapped with Bowtie). But I

[galaxy-user] 答复: FTP upload problem

, 2012 11:25 AM 收件人: Yan He 抄送: galaxy-user@lists.bx.psu.edu 主题: Re: [galaxy-user] FTP upload problem Hello Yan, This was a problem on our end that should be resolved now. Please try to FTP again and be sure to let us know if problems persist or return. Our apologies for the inconvenience, Jen

[galaxy-user] extract genome sequence

Hi everyone, I have the genome sequence and gene annotation file. Is there a tool on Galaxy to extract the 5,000 bp upstream, 5,000 bp downstream and genome sequences of the genes (including exons and introns) from the genome sequence? Any suggestions are highly appreciated! Thanks! Yan

[galaxy-user] How to do an GO enrichment analysis in Galaxy?

Hi everyone, I got a list of differentially expressed genes from my RNA-seq data. Is there a tool on Galaxy that I can do the GO enrichment analysis for the differentially expressed genes? Any help or suggestion is highly appreciated! Best regards, Yan

[galaxy-user] 答复: How to do an GO enrichment analysis in Galaxy?

are highly represented in the data. Is there a tool in Galaxy to fulfill this? Thanks again, Yan -邮件原件- 发件人: Björn Grüning [mailto:bjoern.gruen...@pharmazie.uni-freiburg.de] 发送时间: Monday, October 08, 2012 2:06 PM 收件人: Yan He 抄送: galaxy-user@lists.bx.psu.edu 主题: Re: [galaxy-user] How

[galaxy-user] Counts of mapped reads for each gene?

Hi Jen and other galaxy-users, I am analyzing our RNA-seq data. First, I mapped the RNA-seq data to the reference genome. I am wondering if there is a tool that could count the number of reads that mapped to each gene. That's important information for my subsequent analysis. Any reply is

[galaxy-user] 答复: Counts of mapped reads for each gene?

Rajkumar Rajamani [mailto:a...@hum-gen.au.dk] 发送时间: Thursday, August 22, 2013 3:14 PM 收件人: Yan He; galaxy-user@lists.bx.psu.edu 主题: RE: [galaxy-user] Counts of mapped reads for each gene? Hi Yan, You may use the HTseq count wrapper in the http://galaxy.nbic.nl/. It does a good job and I could

[galaxy-user] 答复: Counts of mapped reads for each gene?

Hi Anto, Thanks so much! I will try. Best wishes, Yan 发件人: Anto Praveen Rajkumar Rajamani [mailto:a...@hum-gen.au.dk] 发送时间: Thursday, August 22, 2013 3:57 PM 收件人: Yan He; galaxy-user@lists.bx.psu.edu 主题: RE: [galaxy-user] Counts of mapped reads for each gene? Hi Yan, I also

[galaxy-user] exome-capture sequencing analysis tools?

Hi Jen and other Galaxy-users, I am working on exome-capture sequencing with NGS. I am wondering if there is a tool to identify SNPs on Galaxy? I would like to get SNP information (position and allele frequency ) for each gene. Any information is highly appreciated! Thanks! Best wishes,

[galaxy-user] How to extract geneID from pileup file?

Dear galaxy-users, I am working on a project to identify and genotype SNPs in targeted genes. I did some analysis using Galaxy. First, mapping to the genome with Bowtie. Second, identify SNPs using MPileup in SAMtools. When I got the pileup file, the SNP information is in which chromosome and

[galaxy-user] About Slice BAM tool

Hi Jen and other galaxy-users, I was using Slice BAM tool on Galaxy to get the alignment overlap with the targeted intervals. After I got the output BAM file, I used flagstat to get the detailed information of the output BAM file. What I got from flagstat is as following. 13704486 + 0 in

[galaxy-user] How to become admin on Galaxy Cloudman

Hi all, I just established Galaxy Cloudman on Amazon EC2. I would like to add some tools in tool shed to to it. However, I need to be the admin to do this. Once I got into the galaxy cloudman, I had to register a new account and then log in. The admin interface (described in tool shed wiki)

[galaxy-user] How to lauch bulit cluster on Cloudman?

Dear all, I just established Galaxy Cloudman on Amazon EC2. I created a cluster named exon_capture and uploaded a lot of data to it. After some analysis, I terminated the cluster. The second time I wanted to get access to the exon_capture cluster, I created a new instance under the