[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 exon_capture. However, under this instance, the access galaxy button is in grey and not active. I tried several time, but the button was always in grey. Does anyone know what's wrong? Did I miss something? It may be a very simple question, but it bothers me a whole afternoon. Thanks a lot! Yan ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[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) didn't appear at all. How could I log in as admin on Galaxy Cloudman? This may be a very simple question, but it bothers me two days. Looking forward to your replies! Best wishes, Yan ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[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 total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 2989995 + 0 mapped (21.82%:-nan%) 13704486 + 0 paired in sequencing What's the QC-passed reads? What's the mapped reads? Should I only get the mapped reads to the targeted intervals? I am very confused. Any help is highly appreciated! Thanks a lot! Best wishes, Yan ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[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 what position. I would like to focus on the SNPs within genes. How could I extract the SNP information for each genes (SNP position, coverage)? Is there a tool in Galaxy to fulfill this? Any help is highly appreciated! Best wishes, Yan ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] 答复: Counts of mapped reads for each gene?
Hi Anto, Thank you very much for your reply! I tried Galaxy/NBIC. However, I had problem with uploading my files. I used FTP, because the file I had was larger than 2G, but I couldn’t connect to the NBIC FTP. Do you have some idea how to solve the problem? Thanks! Yan 发件人: Anto Praveen 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 employ edgeR on that count matrix. Good luck. Best wishes, Anto ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[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 had problems with NBIC FTP. NBIC allows only 10 GB space for user. I made my BAM files in main server (using Tophat2) and then uploaded them to NBIC using their download URLs. It was fast. It took me less than a hour to move 16 BAM files (around 9.5 GB). You may try this. Good luck. Best wishes, Anto _ From: Yan He [yanh...@hotmail.com] Sent: 22 August 2013 09:36 To: Anto Praveen Rajkumar Rajamani; galaxy-user@lists.bx.psu.edu Subject: 答复: [galaxy-user] Counts of mapped reads for each gene? Hi Anto, Thank you very much for your reply! I tried Galaxy/NBIC. However, I had problem with uploading my files. I used FTP, because the file I had was larger than 2G, but I couldn’t connect to the NBIC FTP. Do you have some idea how to solve the problem? Thanks! Yan 发件人: Anto Praveen 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 employ edgeR on that count matrix. Good luck. Best wishes, Anto ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[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, Yan ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[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 highly appreciated! Thanks, Yan ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] 答复: How to do an GO enrichment analysis in Galaxy?
Hi Bjoern, Thank you very much for your reply! I am working on one species of oyster and the gene_ids are created from the transcriptome dataset, which is in our own defined format. I already have the gene_ids and GO annotation for each gene. I would like to do the GO enrichment to see which 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 to do an GO enrichment analysis in Galaxy? Hi Yan, have a look at the blast2GO wrapper in the toolshed. If you already have gene-ids you can download the GO in an appropriate format and intersect with your ids. Hope that works, Bjoern 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 ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] 答复: FTP upload problem
Hello everyone, The FTP upload problem come back again. I kept receiving the error message “530 Sorry, the maximum number of clients (3) for this user are already connected.” Anyone can help? Thanks! Yan -邮件原件- 发件人: Jennifer Jackson [mailto:j...@bx.psu.edu] 发送时间: Saturday, August 11, 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 team On 8/8/12 11:03 PM, Yan He wrote: 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! Yan ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 got the following error message: An error occurred running this job: cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 10 --FDR 0.05 /galaxy/main_pool/pool4/files/004/800/dataset_4800173.dat /galaxy/main_pool/pool3/files/004/799/dataset_4799827.dat /galaxy/main_pool/pool4/files/004/799/dataset_4799831.dat Where did I do wrong? Thanks very much for your help! Yan ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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! Yan ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[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 ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
