Re: [galaxy-user] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
Hi Uma, If you look under 'NGS Mapping' there is 'Map with Bowtie for SOLiD' and 'Map with BWA for SOLiD' They take fastq, but you can use 'NGS: QC and manipulation' 'Convert' to generate a fastq file from fastqc and qual files. Or at least you could for SOLiD4 files. Ian From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Chandran, Uma [chandra...@upmc.edu] Sent: 11 March 2014 13:14 To: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data? Are there mappers for SoLiD 5500 on Galaxy? If so, do they take csfasta files as input? Thanks Uma Chandran ___ 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 output
I am quite new to RNA-seq analysis, but what I have learned so far is that replicates are important. If you have this result with no replicates then P-values are more or less meaningless. You can also gauge what is happening by looking at the modelled read count output. If the counts are both less than 50ish you are unlikely to have a robust result for that gene/transcript. Ian From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Malik, Shivani [shivani.ma...@ucsf.edu] Sent: 11 March 2014 21:43 To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Cuffdiff output Hi, I have a question about interpreting the cuffdiff data and how to pick up significant genes. I have genes which show ~8 fold change between 2 conditions: eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is threshold of FPKM below which Cuffdiff does not consider it an FPKM to be valid and hence significance in no? What downstream analysis should I use to extract a meaningful list of genes from the Cuffdiff data? Also, I filtered out FPKMs which were below 5 in both conditions? Is that reasonable? Thanks Shivani ___ 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/
[galaxy-user] Zooming in and out in Circster
Sorry if I am missing some instructions somewhere, but how do you zoom out of a Circster plot? I have zoomed in by double clicking, but cannot work out how to zoom back out? Thanks, Ian ___ 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] Problem with workflow step ordering
When i create a GALAXY workflow the order of the steps in the summary are fine until the main pipeline diverges into multiple branches. Then the steps from the different branches get shuffled in the summary and it is difficult to see what is going on. Q. Is it possible to manually reorder steps in a GALAXY workflow summary? There used to a problem where workflows with multiple inputs would randomise the order of the inputs each time the workflow was run. Now the proximity of the inputs to the top left-hand edge of the workflow dictates the precedence. Also, if i manually run the steps one at a time in order in a history and create a workflow from that, in the creation summary (just before making the workflow) everything is in order, however when the workflow is run the order has been messed up. Thanks, Ian ___ 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] CEAS in Galaxy
Cistrome (instance of GALAXY) has CEAS included. Ian From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Jennifer Jackson [j...@bx.psu.edu] Sent: 08 November 2011 22:43 To: shamsher jagat Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] CEAS in Galaxy Hello, This particular tool group from is not incorporated, but many similar components exist as tools in Galaxy. In particular, the Operate on Genomic Intervals - Profile Annotations for a set of genomic intervals tool may be useful. If not, then importing a gene track (UCSC, ENSEMBL, etc.) and using the other operations in this tool group can bring together annotation features. Hopefully this gives some options for your project, Jen Galaxy team On 11/8/11 1:58 PM, shamsher jagat wrote: Is there an option of running CEAS tool in Galaxy I want to annotate selected enriched regions of ChIP seq data with gene names etc? 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] Q about 'Compute' tool
Thank Russell for the tip, it was just what i needed. Is there a explanation of how to construct the instructions for 'Compute' somewhere? I have not been able to find it. Also thanks to Hans-Rudolf. Ian From: Russell Bell [russell.b...@hci.utah.edu] Sent: 10 October 2011 18:16 To: galaxy-user@lists.bx.psu.edu; Ian Donaldson Subject: Re: [galaxy-user] Q about 'Compute' tool Ian, using your chr15001000geneA.+ chr120002500geneB.- problem i was able to get chr15001000geneA.+ 500.0 chr120002500geneB.- 2500.0 Using c2 if c6=='+' else c3 in the Compute tool. See if it works for you. - Russell Date: Mon, 10 Oct 2011 17:36:58 +0200 From: Hans-Rudolf Hotz h...@fmi.ch To: Ian Donaldson ian.donald...@manchester.ac.uk, Daniel Blankenberg d...@bx.psu.edu, galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Q about 'Compute' tool Message-ID: 4e93111a.4060...@fmi.ch Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 10/10/2011 04:45 PM, Ian Donaldson wrote: Thanks, but not quite what i need. If i start with two intervals: chr15001000geneA.+ chr120002500geneB.- I want to add via, e.g. 'Compute', the TSS position to the end of each line. The desired result being: chr15001000geneA.+500 chr120002500geneB.-2500 This is because geneA is on the '+' strand and geneB is on the '-' strand. Hi Ian Have you tried Filter and Sort- Filter data on any column using simple expressions and create two lists containing all genes on the '+' strand and alles genes on the '-' strand. followed by Text Manipulation- Cut columns from a table using 'c1,c2,c3,c4,c5,c6,c2' for the list with all genes on the '+' strand and using 'c1,c2,c3,c4,c5,c6,c3' for the list with all genes on the '-' strand and then you can create a single list again with Text Manipulation- Concatenate datasets tail-to-head I guess this is waht you want, isn't-it? Regards, Hans Thanks, Ian From: Daniel Blankenberg [d...@bx.psu.edu] Sent: 10 October 2011 14:34 To: Ian Donaldson Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Q about 'Compute' tool Hi Ian, Under Operate on Genomic Intervals, you can try the Get Flanks tool; you can request upstream, downstream, or both of your provided regions. Please let us know if you need additional assistance. Thanks for using Galaxy, Dan On Oct 10, 2011, at 6:35 AM, Ian Donaldson wrote: Hi, Can 'if' statements by used in 'Text manipulation' 'Compute'? The reason is that i have a interval file of UCSC genes, i want to identify the TSS of each and make a new interval reflecting the TSS position for each gene. But because the TSS of a '-' stranded gene is actually the 'end' coord i want to be able to check the strand in the compute statement. Is this possible or is there an easier way to do this inside GALAXY? Thank you, Ian ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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 mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user End of galaxy-user Digest, Vol 64, Issue 9 ** ___ 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
[galaxy-user] Q about 'Compute' tool
Hi, Can 'if' statements by used in 'Text manipulation' 'Compute'? The reason is that i have a interval file of UCSC genes, i want to identify the TSS of each and make a new interval reflecting the TSS position for each gene. But because the TSS of a '-' stranded gene is actually the 'end' coord i want to be able to check the strand in the compute statement. Is this possible or is there an easier way to do this inside GALAXY? Thank you, Ian ___ 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/
