Re: [galaxy-user] Data sources don't load in Firefox
Hi Carrie, We are aware of this new issue with the Firefox 23.0.1 update. Using an alternate browser is recommended to avoid the problem with direct https-http connections, as several of Galaxy's Get Data tools/sources are impacted. Our team is reviewing solutions at a priority. Hopefully this helps to confirm the issue, and our apologies for the current inconvenience, Jen Galaxy team On 9/11/13 8:01 AM, Ganote, Carrie L wrote: Hi List, I'm trying to go through Galaxy 101, and the first step is halting me (UCSC Main table browser does nothing on click). I'm giving a presentation on how to use Galaxy, but the data sources do not load when using Firefox. The tool click registers, because the history pane is minimized, but the URL is not invoked (no activity from browser). I went through my FF settings to see if I'm doing anything to block iframe loads. The funny thing is, though UCSC and BX don't load, but Biomart does - likely because it is not in an iframe but gets loaded as its own window. If I open in a new tab, it's fine. These things load on Chrome, IE and Safari. A lot of my users use Firefox, however. I appreciate any insight into this. Sincerely, Carrie Ganote ___ 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] (no subject)
Hi Maria, This message indicates that an error occurred on the cluster node processing the job. Normally these are not linked to inputs or tools and the general solution is to re-run the job. Please give this a try today - it is possible the error was linked to recent transient server issues. If you continue to have problems after the re-run today, please submit a bug report from the error dataset, leaving inputs and outputs undeleted: http://wiki.galaxyproject.org/Support#Reporting_tool_errors Best, Jen Galaxy team On 9/11/13 12:38 PM, Maria Hoffman wrote: Hello, I am fairly new to galaxy and I am trying to use bowtie2 to map my reads against a custom genome (specifically a ribosomal RNA fasta file). I have formatted the file as suggested in the Galaxywiki ect and I am still getting the following message: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. Any help would me much appreciated! Maria ___ 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] extension of read length
Hi Tobias, In general, you can use *'**NGS: Picard (beta) - SAM to FASTQ'* to extract sequences (convert BAM SAM first), but this tool does not add in extra sequence based off the reference genome (or pad the associated quality scores, etc.). I don't know of a Galaxy wrapped tool that does this, but you might check the Tool Shed, or other public Galaxy servers. Others reading this post may also have advice. Now, going from *BAM* - coordinates (bed/interval) *-* *FASTA* sequence is possible a few ways. The general idea is that the coordinates are manipulated to extend the mapped footprint and then the sequence is extracted from the reference genome. Any content novel in the original sequence is lost, but maybe this still has some utility for you. The two methods below show how to do this, with the 2nd being simpler, if the genome is at UCSC. There are other ways to get flanking sequence, merge/cluster, etc. (see tools in group 'Operate on Genomic Intervals') but below are the most direct methods per-sequence to simply extend. And if you need to filter down multi-mapped data, use the tool ' NGS: SAM Tools - Filter SAM' (converting to/from SAM from BAM as needed). *1st method, works for any genome, include a custom reference genome:* 1 - convert 'NGS: SAM Tools -BAM-to-SAM' 2 - convert SAM to interval with 'NGS: SAM Tools - Convert SAM' or convert to bed with 'BEDTools - Convert from BAM to BED' 3 - split the file into two: one representing the (+) strand alignments, one the (-) using the tool ' Filter and Sort - Filter' 4 - adjust the start or end coordinate to extend the alignment footprint as wanted using the tool 'Text Manipulation - Compute'. Remember that for negative stranded coordinates, the start is really where the end of the sequence aligned and end is where the start of the sequence aligned - interval files report coordinates with respect to (+) strand, smallest - largest. http://wiki.galaxyproject.org/Learn/Datatypes#Interval 5 - cut out the columns to create a standard interval file again, swapping in the new coordinates. Click on the pencil icon to make attribute assignment for columns and to assign a reference genome as needed - this information is required by the next tool. 6 - get the fasta sequence by using the tool 'Fetch Sequences - Extract Genomic DNA' 7 - merge all fasta results together with the tool 'Text Manipulation - Concatenate datasets' 8 - if you need fastq format, you can pad out quality scores and create that with the tool 'NGS: QC and manipulation - Combine FASTA and QUAL' *2nd method, if the reference genome is at UCSC:* 1 - convert 'BEDTools - Convert from BAM to BED' 2 - click on the view at UCSC main link for the dataset 3 - once at UCSC Browser, the data will show up as a custom track, by default named User Track in the top track group. Click on the track name - it will take you to the track controls and focus the browser on this track. 4 - in the top blue menu bar, click on Tools - Table Browser. This track will now be pre-loaded in the form with all options probably set as you want them (this user track is selected and region is genome) - except for one - change output format from BED to be sequence 5 - confirm that the Galaxy box is checked, and click on get output 6 - the next form has options for extending the sequence at 5' and/or 3' ends, all in one go, adjust as you want 7 - click on Send query to Galaxy and the dataset will load back into the working history 8 - the fasta can be converted to fastq as in the 1st method, step #8 Hopefully some of this is helpful! Jen Galaxy team On 9/11/13 1:56 AM, Tobias Hohenauer wrote: Dear all, I am working on an MNAse-Seq experiment with 50bp single end reads. To identify nucleosome positions, I read that one needs to extend the single reads to approximately the length of nucleosome protected DNA, being approximately 150bp. Is there a way in Galaxy to extend 50bp reads to 150bp length, lets say from a .BAM file with mapped reads? Of course any other comment on this topic is much appreciated! Thank you very much, Tobias -- 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] display at ucsc error
Hey there, I am trying to add a custom track of a bed file through Galaxy and i keep getting this error: - Error line 325149 of https://main.g2.bx.psu.edu/root/display_as?id=11632524display_app=ucscauthz_method=display_at: chrM_rCRS not a recognized sequence (note: sequence names are case sensitive) it happens Whether i try to upload the file as a track directly or if i do via Galaxy options. Any one knows anything about this issues? 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] display at ucsc error
Please note, this sequence chrM_rCRS does not exist in the human/hg19 genome browser at UCSC. It is not a recognized sequence. There is a note about this on the gateway page: http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19 See the paragraph titled: Note on chrM --Hiram On 9/12/13 1:25 AM, lilach noy wrote: Hey there, I am trying to add a custom track of a bed file through Galaxy and i keep getting this error: - Error line 325149 of https://main.g2.bx.psu.edu/root/display_as?id=11632524display_app=ucscauthz_method=display_at: chrM_rCRS not a recognized sequence (note: sequence names are case sensitive) it happens Whether i try to upload the file as a track directly or if i do via Galaxy options. Any one knows anything about this issues? 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/
[galaxy-user] About Slice BAM tool
Hi Jen and other galaxy-users, I was using Slice BAM tool on Galaxy to get the alignment overlap with the targeted intervals. After I got the output BAM file, I used flagstat to get the detailed information of the output BAM file. What I got from flagstat is as following. 13704486 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 2989995 + 0 mapped (21.82%:-nan%) 13704486 + 0 paired in sequencing What's the QC-passed reads? What's the mapped reads? Should I only get the mapped reads to the targeted intervals? I am very confused. Any help is highly appreciated! Thanks a lot! 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/
[galaxy-user] de novo RNA-Seq workflow
Hi guys, I am looking for a de novo RNA-seq workflow that uses trinity. Any idea if there is one available? Bests, Carlos Carlos Canchaya ccanch...@gmail.com ___ 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/
