[galaxy-user] ILLumina 1.9 Hiseq
Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is EncodingSanger / Illumina 1.9 now i want to groom my file, but groomer does not have option for 1.9 in Input FASTQ quality scores type any idea which option i should select to grroom my file, later i want to run Bowtie or Tophat, 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/
Re: [galaxy-user] ILLumina 1.9 Hiseq
Hello, The input quality score type should be set as Sanger for your data. Thanks! Jen Galaxy team On 2/29/12 7:39 AM, Ateequr Rehman wrote: Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is Encoding Sanger / Illumina 1.9 now i want to groom my file, but groomer does not have option for 1.9 in Input FASTQ quality scores type any idea which option i should select to grroom my file, later i want to run Bowtie or Tophat, 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-user] ILLumina 1.9 Hiseq
Hi Jen, I have a related question. If Illumina 1.9 is already in Sanger format, is it still necessary to groom the FASTQ files for TopHat? Would it be enough to directly change the data type to Sanger without grooming? Thanks, Carlos On Wed, Feb 29, 2012 at 10:57 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello, The input quality score type should be set as Sanger for your data. Thanks! Jen Galaxy team On 2/29/12 7:39 AM, Ateequr Rehman wrote: Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is Encoding Sanger / Illumina 1.9 now i want to groom my file, but groomer does not have option for 1.9 in Input FASTQ quality scores type any idea which option i should select to grroom my file, later i want to run Bowtie or Tophat, 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-user] ILLumina 1.9 Hiseq
Hi Rich, Tools will allow grooming to be skipped if the data is already in fastqsanger or fastqcssanger format (as appropriate). This can be set at upload or on the Edit Attributes form (pencil icon). For Illumina, these would be data resulting from the CASAVA 1.8+ pipeline. For Illumina 1.5, select Illumina 1.3-1.7 on the FASTQ Groomer tool form to properly format the data. Thanks for bringing up a good topic! Not having to groom can save both time and disk space. Best, Jen Galaxy team On 2/29/12 8:24 AM, Richard Mark White wrote: I have a question about the groomer. Do all Illumina runs need to be groomed, or are there situations where it can be skipped?? (My data says illumina 1.5, so ive been picking input type as illumina 1.3-1.5.) rich *From:* Jennifer Jackson j...@bx.psu.edu *To:* Ateequr Rehman atee...@yahoo.com *Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu *Sent:* Wednesday, February 29, 2012 10:57 AM *Subject:* Re: [galaxy-user] ILLumina 1.9 Hiseq Hello, The input quality score type should be set as Sanger for your data. Thanks! Jen Galaxy team On 2/29/12 7:39 AM, Ateequr Rehman wrote: Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is Encoding Sanger / Illumina 1.9 now i want to groom my file, but groomer does not have option for 1.9 in Input FASTQ quality scores type any idea which option i should select to grroom my file, later i want to run Bowtie or Tophat, Thanks ** ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-user] Visualise data
Hi Ateeq, Please share a link to your history so that we can provide feedback. Use Options - Share or Publish, generate the share link (first button), copy the link into a reply email, and send that back to me directly. Also, your last few questions have been sent as replies to other questions on the mailing list with a new subject line. This causes them to thread/track incorrectly (and potentially be missed). When sending a new question, please start with a brand new message, address the to as galaxy-u...@bx.psu.edu and this will reach us correctly. Thank you and I will watch for your reply, Jen Galaxy team On 2/29/12 11:30 AM, Ateequr Rehman wrote: Hello Admin and users i wanted to visualize my data, i ran Tophat and converted sam to BAM and then cufflink, but totally unable to see any output data, any suggestion, how i could see my results For administrators, on my account run number 76 to 79 are the run i want to visualize Thanks Ateeq ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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] March 2012 Galaxy Update
Hello all, The March 2012 Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02is now available. *Galaxy Update http://wiki.g2.bx.psu.edu/GalaxyUpdates* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates * complements the *Galaxy Development News Briefshttp://wiki.g2.bx.psu.edu/DevNewsBriefs * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - 28 New Papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#New_Papers - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Who.27s_Hiringat four different institutions - Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Upcoming_Events_and_Deadlines - GCC2012 Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#GCC2012_Update, including - Abstract submission is open. - Training Day topics are set. - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Tool_Shed_Contributions If you have anything you would like to see in the April *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates *, please let me know. Thanks, Dave C. -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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/
Re: [galaxy-user] Visualise data
Hi Ateeq, The BAM/SAM files can be visualized in Trackster, using your custom reference genome (the same dataset as used for Bowtie or TopHat). But, there are no Cufflinks results, and therefore nothing to visualize, due to the parameters used. Since you are working with a bacterial genome, the parameters will need to be tuned to account for the lack of transcript splicing. The best resources for advice are likely seqanswers or the tool authors, as explained in this prior answer to another bacterial genome/RNA-seq question: http://galaxy-users-list-archive.2308625.n4.nabble.com/Cufflinks-merging-more-than-one-transcript-on-bacterial-genomes-td4323709.html Recently, there has been some user discussion about RNA-seq analysis and bacterial genomes on the galaxy-user mailing list. If you want to search and read through the QA, using our custom google search is the best way to locate the threads (but, expect to find just a few): http://galaxy.psu.edu/search/mailinglists/ If anyone else reading this thread has help to offer, please feel free to jump in and share any working knowledge for this type of analysis. Best wishes for your project, Jen Galaxy team On 2/29/12 12:31 PM, Ateequr Rehman wrote: hello Jennifer Thanks a lot, here is the link Best ateeq *From:* Jennifer Jackson j...@bx.psu.edu *To:* Ateequr Rehman atee...@yahoo.com *Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu *Sent:* Wednesday, February 29, 2012 9:24 PM *Subject:* Re: [galaxy-user] Visualise data Hi Ateeq, Please share a link to your history so that we can provide feedback. Use Options - Share or Publish, generate the share link (first button), copy the link into a reply email, and send that back to me directly. Also, your last few questions have been sent as replies to other questions on the mailing list with a new subject line. This causes them to thread/track incorrectly (and potentially be missed). When sending a new question, please start with a brand new message, address the to as galaxy-u...@bx.psu.edu mailto:galaxy-u...@bx.psu.edu and this will reach us correctly. Thank you and I will watch for your reply, Jen Galaxy team On 2/29/12 11:30 AM, Ateequr Rehman wrote: Hello Admin and users i wanted to visualize my data, i ran Tophat and converted sam to BAM and then cufflink, but totally unable to see any output data, any suggestion, how i could see my results For administrators, on my account run number 76 to 79 are the run i want to visualize Thanks Ateeq ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
