Re: [galaxy-user] new cuffdiff with readgroup problem
Hi Jen, I know read_group_tracking files are included now as I say in my e-mail below (before 11 output files now 15 from your cuffdiff) but the question was if also the count_tracking and/or read_group.info files are needed for plotting replicate data in CummeRbund, since I do not succeed with the current output. So now there is no difference what you can do (at least in CummeRbund) with the output compared to when it was 11 output files...? Even though you can choose include Read Group Dataset as I do. Thanks, Johanna From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, November 15, 2013 10:23 PM To: Johanna Sandgren Cc: galaxy-user@lists.bx.psu.edu; Jeremy Goecks Subject: Re: [galaxy-user] new cuffdiff with readgroup problem Hi Johanna, Update: I had this incorrect, the option to include Read Group files in the output is now available and near the bottom on the Cuffdiff tool form input option. Count tracking files are still in the list of open to-do items. Big thanks to Jeremy for the update! Jen Galaxy team On 11/14/13 2:05 PM, Jennifer Jackson wrote: Hi Johanna, Adding in the read_groups and other select output files is a planned enhancement for a future date. The Trello ticket to follow progress is here: https://trello.com/c/lIdpOZ88 related to : https://trello.com/c/U7nceKdj Good question! Jen Galaxy team On 11/12/13 12:26 AM, Johanna Sandgren wrote: Hello, Thanks for your answer. I can see that compared to the output from cuffdiff according to their manual (http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff) there are still files missing from galaxy's output. Like the count tracking files and read_groups.info. So these are vital for replicate plotting in CummeRbund then? When will you also include them in your output? Regards, Johanna From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Thursday, October 31, 2013 4:09 AM To: Johanna Sandgren Cc: galaxy-user@lists.bx.psu.edumailto:galaxy-user@lists.bx.psu.edu; Jeremy Goecks Subject: Re: [galaxy-user] new cuffdiff with readgroup problem Hello Johanna, Last time I checked, this specific functionality was not fully implemented yet. I do not believe that a firm timeline has been set yet for completion. Jeremy can comment if I have this incorrect, but I wanted to get back to you so that you were not wondering! Take care, Jen Galaxy team On 10/21/13 8:54 AM, Johanna Sandgren wrote: Hi, I have tested the new cuffdiff version in galaxy and was very eager to now also get the replicate data for each test. Have anyone tried that yet and succeeded with replicates in downstream R package CummeRbund? Even though I successfully build database with the now 15 output files (including read group tracking), no error message, I can not plot anything with replicates=T. Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near from: syntax error) Anyone know the problem? Thanks, Johanna .. 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/ -- 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features
Re: [galaxy-user] new cuffdiff with readgroup problem
Hello, Thanks for your answer. I can see that compared to the output from cuffdiff according to their manual (http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff) there are still files missing from galaxy's output. Like the count tracking files and read_groups, info. So these are vital for replicate plotting in CummeRbund then? When will you also include them in your output? Regards, Johanna From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Thursday, October 31, 2013 4:09 AM To: Johanna Sandgren Cc: galaxy-user@lists.bx.psu.edu; Jeremy Goecks Subject: Re: [galaxy-user] new cuffdiff with readgroup problem Hello Johanna, Last time I checked, this specific functionality was not fully implemented yet. I do not believe that a firm timeline has been set yet for completion. Jeremy can comment if I have this incorrect, but I wanted to get back to you so that you were not wondering! Take care, Jen Galaxy team On 10/21/13 8:54 AM, Johanna Sandgren wrote: Hi, I have tested the new cuffdiff version in galaxy and was very eager to now also get the replicate data for each test. Have anyone tried that yet and succeeded with replicates in downstream R package CummeRbund? Even though I successfully build database with the now 15 output files (including read group tracking), no error message, I can not plot anything with replicates=T. Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near from: syntax error) Anyone know the problem? Thanks, Johanna .. 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/ -- 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] new cuffdiff with readgroup problem
Hi, I have tested the new cuffdiff version in galaxy and was very eager to now also get the replicate data for each test. Have anyone tried that yet and succeeded with replicates in downstream R package CummeRbund? Even though I successfully build database with the now 15 output files (including read group tracking), no error message, I can not plot anything with replicates=T. Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near from: syntax error) Anyone know the problem? Thanks, Johanna .. 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/
[galaxy-user] New cuffdiff- no result files
Hi, I have this week used the new wrapper version of Cuffdiff that you provide that should now include replicate information in output. But there is no resulting files created. Why? I get all the results in the right panel as usual and they are green (no error message) but the they are all empty.. I use bam-files and cuffmerge files that I have gotten result from before (both in spring and during summer- when you upgraded cuffdiff version). I attach below info for one resulting output. Kind regards, Johanna Tool: Cuffdiff Name: Cuffdiff on data 684, data 384, and others: transcript FPKM tracking Created: Oct 09, 2013 Filesize: 0 bytes Dbkey: hg19 Format: tabular Galaxy Tool Version: 0.0.6 Tool Version: cuffdiff v2.1.1 (4046M) Tool Standard Output: stdouthttps://usegalaxy.org/datasets/bbd44e69cb8906b581bffe7ea9e0cd97/stdout Tool Standard Error: stderrhttps://usegalaxy.org/datasets/bbd44e69cb8906b581bffe7ea9e0cd97/stderr Tool Exit Code: 0 API ID: bbd44e69cb8906b581bffe7ea9e0cd97 Input Parameter Value Note for rerun Transcripts 684: Cuffmerge on data 559, data 618, and others: merged transcripts Name MBs Add replicate 261: MarkDups_Dupes Marked s101_ok.bam Add replicate 348: s102_MarkDups_Dupes Marked on 256.bam Add replicate 412: s103MarkDups_Dupes Marked 357.bam Add replicate 378: s104MarkDups_Dupes Marked 347.bam Add replicate 425: s105MarkDups_Dupes Marked.bam Name Ctrls Add replicate 701: MarkDups_Dupes Marked688.bam Add replicate 671: SRR112675MarkDups_Dupes Marked417.bam Add replicate 433: SRR112673MarkDups_Dupes Marked 343.bam Add replicate 427: SRR111937MarkDups_Dupes Marked 376.bam Add replicate 382: SRR112601MarkDups_Dupes Marked 316.bam Add replicate 384: SRR111936MarkDups_Dupes Marked 328.bam Library normalization method geometric Dispersion estimation method pooled False Discovery Rate 0.05 Min Alignment Count 5 Use multi-read correct Yes Perform Bias Correction Yes Reference sequence data cached Include Read Group Datasets Yes Set Additional Parameters? (not recommended for paired-end reads) No .. 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] Cuffdiff changes
Thanks for quick reply. Where can I see which version are being used? It does not say in the attached (in my first e-mail) info-view after the run.. What does Cuffdiff (version 0.0.5) mean then? What version was it before? It is a great difference in number of DE genes.. I mostly meant it was the same now in August with more DE genes for all different type of analysis that I have previously done (consistent new results with no settings changed), I really do not see more DE genes when 5 vs 6 samples compared to 1 vs 2 samples. But that might be due to more biological reasons. I look forward to the update, will that mean another version of Cuffdiff again? Kind regards, Johanna From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Thursday, August 22, 2013 8:04 PM To: Johanna Sandgren Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Cuffdiff changes I am wondering why Cuffdiff suddenly gives many more significant DE genes? Cuffdiff was recently updated to version 2.1.0; this update likely explains the different results that you see. I have rerun several analysis, also with more samples in each group, all give much more significant genes. Why? More samples = more power to accurately estimate expression levels = more DE genes. Also, will replicate information soon be included in output files? Replicate data will be available when we next update our server. This should occur in about 3 weeks. Best, J. ___ 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/
[galaxy-user] replicates in cuffdiff output
Hi, I am running cufflinks and cuffdiff using Galaxy. I am however wondering if it is not supposed to be output files from cuffdiff regarding each replicate. Anyone know why those (read.group-files) are not there, or when they will be if it is because of the version used in Galaxy. I find it very valuable to have those to be able to see intra/inter-group features in downstream analysis. Thanks, Johanna .. 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/
