[galaxy-user] TopHat version in GALAXY
Dear all: I have GALAXY installed in a UNIX server. BOWTIE works fine but TOPHAT and CUFFDIFF crash upon starting. In the case of TOPHAT, I noticed that GALAXY has a 1.5.0 version integrated, while the TOPHAT website claims the latest version is 1.4.1. My question is which are the best/appropiate TOPHAT and CUFFDIFF versions? The error message I get is TOPHAT not recognized. Any other suggestions? Thanks, G. ___ 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] questions on directionality
Nick, I apologize if this is covered in documentation or help threads. searched and it seemed it was not. I have several illumina rna-seq data sets that should be directional. It seems the directionality is very good, based on the visualization. First question is; in the visualization window, are the reads color coded by direction, i.e. are orange one direction and blue the other? Different colors in read data does indicate strandedness; hover over the track and click on the 'Edit Settings' icon (gear) to see/change the sense/anti-sense colors used. Similar question, is there a way to quantify directionality of the data set? You can use the Filter SAM tool to filter for mapped strand. Good luck, 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/
Re: [galaxy-user] Convert SAM to bigwig
Hi Stephen, The options in the prior post are still current for the Galaxy main server, however a direct method is something the team would like to consider. I have opened a ticket a bitbucket to track progress: http://bitbucket.org/galaxy/galaxy-central/issue/727/add-a-tool-to-do-bam-to-bigwig-to-galaxy Thanks for bringing up this topic again, it is a great idea, Best, Jen Galaxy team On 2/27/12 3:05 AM, Stephen Taylor wrote: Hi, What is the 'official' method of converting a BAM file to a bigwig on the public server? I saw this post: http://gmod.827538.n3.nabble.com/SAM-to-bigbed-td3059499.html but it seems a bit long winded given the commonness of the operation. On our local galaxy we installed from the Tool Shed: BAM to BigWig Calculates coverage from a BAM alignment file Which seems the obvious choice to make available. Thanks, Steve ___ 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] demultiplex Miseq data with separate index file.
I am using Galaxy main site to analyse MiSeq data of pooled samples. Essentially the run produces 3 fastq files consisting of R1, R2 read files and a separate index file. They are in the format below. R1: @M00132:6:0-A0JG4:1:1:18014:1842 1:N:0:0 Sequence data R2: @M00132:6:0-A0JG4:1:1:18014:1842 2:N:0:0 Sequence data Index: @M00132:6:0-A0JG4:1:1:18014:1842 1:N:0:0 CTCGGT + @@DFD I would like to use Galaxy to demultiplex the samples and then analyse them individually. I have found barcode Splitter (version 1.0.0) on Galaxy however this tool requires the index to be found at the beginning of the sequence. Therefore I am attempting to add the index sequence onto the end of the sequence read data. FASTQ joiner (version 1.0.0) joins fastq files, however the fastqs to be joint must be distinguished by a /1 or /2 at end of sequence identifiers. Does anyone have any advice or experience of demultiplexing data in this format? Thanks, Phil DISCLAIMER: The information in this message is confidential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorised. If you are not the intended recipient, any disclosure, copying, or distribution of the message, or any action or omission taken by you in reliance on it, is prohibited and may be unlawful. Please immediately contact the sender if you have received this message in error. Thank you.___ 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] FASTQ groomer processing time
I used FASTQ groomer on a 29 Gb Illumina 1.5+ FASTQ file to go from Illumina 1.3-1.7+ to Sanger and it is still processing after over 30 hrs. Is this a normal time frame for a FASTQ file this size ? Matthew The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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] demultiplex Miseq data with separate index file.
Phil, we also have a MiSeq and currently experienced the same phenomenon how to demultiplex. We have our local galaxy instance and wrote some scripts to efficiently demultiplex the sample. However, you FIRST need to convert on the MiSeq the primary fastq into a (in their view) multiplex identified fastq. There the final :0 in all your headers get converted in the multiplex or sample ID you gave it in the sample sheet! I see you all have zeros which is not quite helpfull. After the samplesheet conversion we just concat all fastq files which you then can easily group the reads on the final multiplex id en demultiplex it in separate files. In addition you can split the forward and reversed by the space1 and space2 identifyers in the header. Many tools do not require the conversion to /1 and /2 any more but this can be easily done locally with for instance sed on unix. We converted it like this: @M00132:6:0-A0JG4:1:1:18014:1842 1:N:0:2 @M00132:6:0-A0JG4:1:1:18014:1842 2:N:0:2 into @M00132:6:0-A0JG4:1:1:18014:1842/1 1:N:0:2 @M00132:6:0-A0JG4:1:1:18014:1842/2 2:N:0:2 Since many tools grep till the first space. I might pop the scripts soon in the toolshed but that might not be of great help maybeotherwise pm me and I send you the script (perl). Alex Van: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] namens Philip Dean [philip.d...@nbt.nhs.uk] Verzonden: maandag 27 februari 2012 19:45 To: 'galaxy-u...@bx.psu.edu' Onderwerp: [galaxy-user] demultiplex Miseq data with separate index file. I am using Galaxy main site to analyse MiSeq data of pooled samples. Essentially the run produces 3 fastq files consisting of R1, R2 read files and a separate index file. They are in the format below. R1: @M00132:6:0-A0JG4:1:1:18014:1842 1:N:0:0 Sequence data R2: @M00132:6:0-A0JG4:1:1:18014:1842 2:N:0:0 Sequence data Index: @M00132:6:0-A0JG4:1:1:18014:1842 1:N:0:0 CTCGGT + @@DFD I would like to use Galaxy to demultiplex the samples and then analyse them individually. I have found barcode Splitter (version 1.0.0) on Galaxy however this tool requires the index to be found at the beginning of the sequence. Therefore I am attempting to add the index sequence onto the end of the sequence read data. FASTQ joiner (version 1.0.0) joins fastq files, however the fastqs to be joint must be distinguished by a /1 or /2 at end of sequence identifiers. Does anyone have any advice or experience of demultiplexing data in this format? Thanks, Phil DISCLAIMER: The information in this message is confidential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorised. If you are not the intended recipient, any disclosure, copying, or distribution of the message, or any action or omission taken by you in reliance on it, is prohibited and may be unlawful. Please immediately contact the sender if you have received this message in error. Thank you. ___ 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] FASTQ groomer processing time
Matthew, yes we have seen such kind of long runs before (depending on server load). Happy most of our reads are now in 1.8+ format. You can parallelise the process by splitting the file in 4 or 6 and submit for grooming and afterwards merge them again... Alex Van: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] namens Matthew McCormack [mccorm...@molbio.mgh.harvard.edu] Verzonden: maandag 27 februari 2012 21:13 To: galaxy-user@lists.bx.psu.edu Onderwerp: [galaxy-user] FASTQ groomer processing time I used FASTQ groomer on a 29 Gb Illumina 1.5+ FASTQ file to go from Illumina 1.3-1.7+ to Sanger and it is still processing after over 30 hrs. Is this a normal time frame for a FASTQ file this size ? Matthew The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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/
