Re: [galaxy-user] problems with TOPHAT in Galaxy
Hello Amit, The output files created by Tophat are listed on the tool form: accepted_hits.bam, junctions.bed, insertions.bed and deletions.bed This is NGS data input? Do you mean that no data in the results (accepted_hits.bam - could convert to SAM to check) include the "XS" tag? If no result/tags, then spliced data is not mapping. Reviewing the advanced parameters would be helpful, but I would start with the quality of the input data (run FastQC). It may be that some trimming is needed (run Trim). Thanks, Jen Galaxy team On 11/7/13 1:53 AM, Amit Pande wrote: Hi, I am trying to align long RNA fatsq formatted files from ENCODE project generated by CSHL. The problem I am encountering is that there is no XS file being generated which can be taken for further processing with samtools. Kindly help. warm regards, Amit. ___ 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] problems with TOPHAT in Galaxy
Hi, I am trying to align long RNA fatsq formatted files from ENCODE project generated by CSHL. The problem I am encountering is that there is no XS file being generated which can be taken for further processing with samtools. Kindly help. warm regards, Amit. ___ 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] problems with Tophat
Hello Elwood, The public Main Galaxy server was very busy this weekend this likely contributed to the problems you were having with loaded and possibly with job execution. First, be sure that you are loading with FTP and confirming that loading is successful with a client during this time. This also permits interrupted loads can be restarted as necessary. http://wiki.galaxyproject.org/FTPUpload For the Tophat job, there were some known job failures related to load. I would restart the job and see if a new run resolves the issue. If the problem is persistent, please submit the new error as a bug report and we can take a closer look. Be sure to leave all inputs and both Tophat runs active (undeleted) if you submit a bug report, as a history is often very helpful/necessary when diagnosing a problem. Sorry that you were having problems, but hopefully these can be resolved quickly. Best, Jen Galaxy team On 5/7/13 6:34 AM, Elwood Linney wrote: Hello, I have successfully used the public server for processing RNAseq data but I have run into some problems this weekend. And this weekend there were various times when I would get a message that Galaxy was not available. Specifically, I received some new 50bp single-ended RNAseq data and proceeded to process it through the public server as I have done successfully before. I concatenated it the subfiles into one fastq file, transferred it to Galaxy, groomed it just to be safe, looked at its quality and did not have to trim it and then I passed it on to Tophat. [all in the same manner that had worked for me before] It consisted of 4, approximately 15gb files. While i was moving these files individuallly into the Tophat stage this weekend there were interruptions in the availability of Galaxy. I waited during the weekend, one set of the 4 Tophat files for one of the 4 datasets was processed but then 1 file that I had processed during the interruption turned out to have errors, so I deleted it and re-entered it, another set was processing overnight and then it turned out to have errors. So thinking that maybe 3 of the 4 sets for some reason had problems, I deleted them, re entered them. One was going overnight and into the day and this morning it had errors. Since i am not sure how to read these errors, I am at a loss as to what is happening, particularly since one of my files was successfully processed through Tophat. This is the readout for one of the 4 Tophat files that were in error. Any advice on this would be welcome since I hope to soon have a 64gb ram computer with 12 cores to transfer Galaxy to. 43: Tophat for Illumina on data 8: accepted_hits error An error occurred with this dataset: /TopHat v1.4.0 tophat -p 8 /galaxy/data/danRer7/bowtie_index/danRer7 /galaxy/main_pool/pool7/files/006/143/dataset_6143636.dat Exception in thread Thread-1: Traceback (most recent call last): File "/usr/global/python/2.6.5/lib/python2.6/threading.py", l/ Sincerely, Elwood Linney Duke University Medical Center ___ 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 Galaxy Support and Training 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] problems with Tophat
Hello, I have successfully used the public server for processing RNAseq data but I have run into some problems this weekend. And this weekend there were various times when I would get a message that Galaxy was not available. Specifically, I received some new 50bp single-ended RNAseq data and proceeded to process it through the public server as I have done successfully before. I concatenated it the subfiles into one fastq file, transferred it to Galaxy, groomed it just to be safe, looked at its quality and did not have to trim it and then I passed it on to Tophat. [all in the same manner that had worked for me before] It consisted of 4, approximately 15gb files. While i was moving these files individuallly into the Tophat stage this weekend there were interruptions in the availability of Galaxy. I waited during the weekend, one set of the 4 Tophat files for one of the 4 datasets was processed but then 1 file that I had processed during the interruption turned out to have errors, so I deleted it and re-entered it, another set was processing overnight and then it turned out to have errors. So thinking that maybe 3 of the 4 sets for some reason had problems, I deleted them, re entered them. One was going overnight and into the day and this morning it had errors. Since i am not sure how to read these errors, I am at a loss as to what is happening, particularly since one of my files was successfully processed through Tophat. This is the readout for one of the 4 Tophat files that were in error. Any advice on this would be welcome since I hope to soon have a 64gb ram computer with 12 cores to transfer Galaxy to. 43: Tophat for Illumina on data 8: accepted_hits error An error occurred with this dataset: *TopHat v1.4.0 tophat -p 8 /galaxy/data/danRer7/bowtie_index/danRer7 /galaxy/main_pool/pool7/files/006/143/dataset_6143636.dat Exception in thread Thread-1: Traceback (most recent call last): File "/usr/global/python/2.6.5/lib/python2.6/threading.py", l* Sincerely, Elwood Linney Duke University Medical Center ___ 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/
