Re: [galaxy-user] Counts of mapped reads for each gene?
Hi, Yan The htseq_bams_to_count_matrix tool in the test toolshed might be worth a try - it creates tabular count matrices from any number of individual sample bam/sam files (it is NOT read group aware!). Each row contains the count for that contig for each sample. It uses HTSeq code and you supply your favourite gene model as a GTF file for defining the regions to count and how to amalgamate - eg count reads overlapping exons and sum those into total counts for each gene. Please give it a try. Install from the admin interface and let me know how you get on. There's a companion tool differential_count_models also in the test toolshed that includes edgeR, DESeq2 and VOOM from Bioconductor - it runs 1 or 2 way GLMs using the count matrices generated by the htseq tool - be warned that it takes a long time to install everything so be patient and allow 20 minutes or so for the installation to finish because it compiles and installs R 3.0.1 and Bioconductor packages. Suggestions for improvement or bug reports always welcomed. Good luck. On Thu, Aug 22, 2013 at 3:35 PM, Yan He yanh...@hotmail.com wrote: 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/ ___ 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/
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, 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/
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] 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/
Re: [galaxy-user] tool within a tool
On Thu, Aug 22, 2013 at 12:07 AM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi, I am wondering if it is possible in Galaxy to design a tool whose sole purpose is to run other tools. This is motivated by our desire to enhance execution capabilities of existing tools via a generic tool which acts as a wrapper. This sounds a bit like the idea of making a workflow into a tool (or act in a tool like manor)... but I think you'd be better off raising this question on the Galaxy Development list: http://lists.bx.psu.edu/pipermail/galaxy-dev/ Peter ___ 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] Cuffdiff changes
Hi, I am wondering why Cuffdiff suddenly gives many more significant DE genes? I have used same input data and now get approx 5x more significant genes, settings is same with the exception that you now included library normalization and dispersion estimation. See below for parameters. I have rerun several analysis, also with more samples in each group, all give much more significant genes. Why? Also, will replicate information soon be included in output files? Kind regards, Johanna Tool: Cuffdiff Tool: Cuffdiff Name: Cuffdiff on data 225, data 236, and others: splicing differential expression testing Name: Cuffdiff on data 225, data 236, and others: splicing differential expression testing Created: 4-Apr-13 Created: 21-Aug-13 Filesize: 10.3 MB Filesize: 10.2 MB Dbkey: hg19 Dbkey: hg19 Format: tabular Format: tabular Galaxy Tool Version: 0.0.5 Galaxy Tool Version: 0.0.5 Tool Version: Tool Version: Tool Standard Output: stdouthttps://main.g2.bx.psu.edu/datasets/bbd44e69cb8906b5355e4a035e92cd84/stdout Tool Standard Output: stdouthttps://main.g2.bx.psu.edu/datasets/bbd44e69cb8906b524bcf7e585f495b1/stdout Tool Standard Error: stderrhttps://main.g2.bx.psu.edu/datasets/bbd44e69cb8906b5355e4a035e92cd84/stderr Tool Standard Error: stderrhttps://main.g2.bx.psu.edu/datasets/bbd44e69cb8906b524bcf7e585f495b1/stderr Tool Exit Code: 0 Tool Exit Code: 0 API ID: bbd44e69cb8906b5355e4a035e92cd84 API ID: bbd44e69cb8906b524bcf7e585f495b1 Input Parameter Value Note for rerun Input Parameter Value Transcripts 261: Cuffmerge on data 258, data 135, and others: merged transcripts Transcripts 261: Cuffmerge on data 258, data 135, and others: merged transcripts Perform replicate analysis Yes Perform replicate analysis Yes Group name s202 Group name s202 Add file 194: Galaxy883-[MarkDups_Dupes_Marked_882_202.bam].bam Add file 194: Galaxy883-[MarkDups_Dupes_Marked_882_202.bam].bam Group name Ctrls Group name Ctrls Add file 236: MarkDups_Dupes Marked216.bam Add file 236: MarkDups_Dupes Marked216.bam Add file 225: MarkDups_Dupes Marked206.bam Add file 225: MarkDups_Dupes Marked206.bam Library normalization method not used (parameter was added after this job was run) Library normalization method geometric Dispersion estimation method not used (parameter was added after this job was run) Dispersion estimation method pooled False Discovery Rate 0.05 False Discovery Rate 0.05 Min Alignment Count 2 Min Alignment Count 2 Perform quartile normalization No Perform quartile normalization No Use multi-read correct Yes Use multi-read correct Yes Perform Bias Correction Yes Perform Bias Correction Yes Reference sequence data cached Reference sequence data cached Set Additional Parameters? (not recommended) Yes Set Additional Parameters? (not recommended) Yes Average Fragment Length 200 Average Fragment Length 200 Fragment Length Standard Deviation 80 Fragment Length Standard Deviation 80 .. Johanna Sandgren, PhD Department of Oncology-Pathology CCK, Karolinska Institutet SE-171 76 Stockholm, Sweden +46-8-517 721 35 (office), +46-8- 321047(fax), +46-708 388476 (mobile) ___ 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/
Re: [galaxy-user] How to get random region of 1000-bp window in the chromosome not overlapping specific [gtf] file
Hello John, Use Make windows with the sliding window option (for example, offset =1), then use Text Manipulation - Select random lines. Best, Jen Galaxy team On 8/22/13 7:06 AM, 师云 wrote: Dear Galaxy develop team: As the subject said, I need to obtain random regions which are 1000-bb, and then filter these regions to remove regions overlapping a specific [gtf] file. So can I obtain random regions with Galaxy? I found (Regional Variation)-Make windows may help me, but the tool doesn't work at random. bests John ___ 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/ -- Jennifer Hillman-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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Clip
Hi, I was using the clip program, but my adapters are on the 5' end. Is there any way to use this program so it will clip the 5' end or a way to make all my reads the reverse complement and run it through this program? Thanks ___ 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/
Re: [galaxy-user] Clip
Hello, The Clip program only acts on the 3' end. In some cases, running FastQC to isolate adapter regions, then using a tool like FASTQ Trimmer or Trim will work (if the lengths are somewhat fixed). Alternately, the tools NGS: QC and manipulation - Reverse-Complement or Manipulate FASTQ will reverse compliment reads. For the second, the option is located in Manipulate Reads - Manipulate on 'Sequence Content' - Sequence Manipulation Type:. There are several options here, including trim again, but also Reverse Complement. Hopefully this helps! Jen Galaxy team On 8/22/13 12:03 PM, William Yarosh wrote: Hi, I was using the clip program, but my adapters are on the 5' end. Is there any way to use this program so it will clip the 5' end or a way to make all my reads the reverse complement and run it through this program? Thanks ___ 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/ -- Jennifer Hillman-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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] How to get random region of 1000-bp window in the chromosome not overlapping specific [gtf] file
Hi Jen, Thank you very much! Best, John From: Jennifer Jackson Sent: Friday, August 23, 2013 12:21 AM To: 师云 Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] How to get random region of 1000-bp window in the chromosome not overlapping specific [gtf] file Hello John, Use Make windows with the sliding window option (for example, offset =1), then use Text Manipulation - Select random lines. Best, Jen Galaxy team On 8/22/13 7:06 AM, 师云 wrote: Dear Galaxy develop team: As the subject said, I need to obtain random regions which are 1000-bb, and then filter these regions to remove regions overlapping a specific [gtf] file. So can I obtain random regions with Galaxy? I found (Regional Variation)-Make windows may help me, but the tool doesn't work at random. bests John ___ 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/ -- Jennifer Hillman-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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Clip
Hello, This Galaxy wrapper is based on the FASTX-Toolkit tool by the same name. A link to the original is at the bottom of the tool's form in the UI. To see the Galaxy wrapper, it is in the source here: galaxy-central / tools / fastx_toolkit https://bitbucket.org/galaxy/galaxy-central Questions about the core tool can be directed to the tool author. Help with running a local Galaxy or tools in general is on the galaxy-...@bx.psu.edu mailing list: http://wiki.galaxyproject.org/Support#Mailing_Lists If you create a new wrapper with more options, please consider contributing it to the Tool Shed, as this tool is super popular and the option for 5' clipping has come up before. http://wiki.galaxyproject.org/Tool%20Shed Take care, Jen Galaxy team On 8/22/13 12:58 PM, William Yarosh wrote: Thanks, I'm trying to figure out how to use these programs. Do you know where I can get the source code for clip? I think I can edit the program to look at the 5' end if I see it. Will On Aug 22, 2013, at 3:19 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello, The Clip program only acts on the 3' end. In some cases, running FastQC to isolate adapter regions, then using a tool like FASTQ Trimmer or Trim will work (if the lengths are somewhat fixed). Alternately, the tools NGS: QC and manipulation - Reverse-Complement or Manipulate FASTQ will reverse compliment reads. For the second, the option is located in Manipulate Reads - Manipulate on 'Sequence Content' - Sequence Manipulation Type:. There are several options here, including trim again, but also Reverse Complement. Hopefully this helps! Jen Galaxy team On 8/22/13 12:03 PM, William Yarosh wrote: Hi, I was using the clip program, but my adapters are on the 5' end. Is there any way to use this program so it will clip the 5' end or a way to make all my reads the reverse complement and run it through this program? Thanks ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.org http://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/ -- Jennifer Hillman-Jackson http://galaxyproject.org -- Jennifer Hillman-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/ 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/
