Re: [galaxy-user] Why is 'Filter pileup' not recegnising my 'Generate pileup' file?
Hi Jacqui, The NGS: SAM Tools - Filter pileup tool was corrected last September to require input datasets to be assigned to the format pileup. Is there a chance that these datasets are not? Maybe imported or manipulated by other tools, resulting in another datatype assignment (tabular or other)? The datatype is noted directly under the dataset name, in each dataset's box in the history. If so, you can reassign the format (as long as it meets specification, see the tool NGS: SAM Tools - Generate pileup for a description), by clicking on the pencil icon for a dataset, then the tab Datatype, and assigning pileup manually (don't forget to save). This will help with tool-input dataset recognition. Should the problem be unrelated to file format, please send in a link to a shared history (on the public Main server) and we can help to troubleshoot from there. You can send this directly to me. From the history panel use: Options (gear icon) - Share or Publish - generate link - copy/paste into email. Best, Jen Galaxy team On 11/22/12 3:16 AM, Jacqui Stockley wrote: Hi, I was wondering if you could help me with a problem I have been having recently. I have carried out a number of NGS analyses using SAM Tools where I have generated pileup and then filtered this file using the filter pileup tool. However, recently when I have tried to do this the filter pileup is not recognising a compatible dataset in the history (ie it is not recognising the generate pileup file). I have always done the same so I can't understand what I might have done wrong. I have gone into old datasets and tried to filter pileups from previous histories and they also do not recognise the generate pileup file despite the fact they have previously! Is there something I am doing majorly wrong or should I be using another function? Many thanks for any help or advice! Jacqui ___ 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://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/
Re: [galaxy-user] BWA mapping with index file from history
Hi Kanwar, To use a custom genome, all you need to load is the .fasta file of the genome. Galaxy will do the indexing as part of the mapping job when it is launched. Help with custom genomes in is this wiki: http://wiki.galaxyproject.org/Support#Custom_reference_genome Hopefully this helps to simplify things! Jen Galaxy team On 11/26/12 2:56 AM, shamsher jagat wrote: I have a Hi-seq Single end data and want to align it to a viral genome and have fasta file of viral genome. I have created index files out side Galaxy (I believe I cannot create index file with in Galaxy). The question which I have is: There are various index files (v.fasta.amb; v.fasta.pac; v.fasta.rbwt; v.fasta.rpac; v.fasta.sa http://v.fasta.sa) should I be using all the these files as zip file for index file or one (which one?). Thanks Kanwar ___ 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://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/
[galaxy-user] Find out sense and antisense sequences
Hi, Galaxy users! I have a question on how to find out sense and antisense sequence. I've got RNA seq data in the fastq format. The sequences inside are partially complementary to each other (complementary is 10nt, while entire is about 30nt). How can I separate these sequences into two groups: sense and antisense (one thing I know is for the sense sequence the 10th nucleotide is always A)? Thanks a lot! Best, Zhiqiang ___ 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] Find out sense and antisense sequences
On Mon, Nov 26, 2012 at 6:47 PM, Zhiqiang Shu z...@bio.fsu.edu wrote: Hi, Galaxy users! I have a question on how to find out sense and antisense sequence. I've got RNA seq data in the fastq format. The sequences inside are partially complementary to each other (complementary is 10nt, while entire is about 30nt). How can I separate these sequences into two groups: sense and antisense Depending on how your sequences were prepared, you might be able to look for a poly-A tail as a clue to orientation. Another approach is to compare the (assembled) transcripts to known genes and if you only get matches on one strand that is probably the correct orientation. (one thing I know is for the sense sequence the 10th nucleotide is always A)? Why is that? Is this related to your library preparation? Peter ___ 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] Find out sense and antisense sequences
Thank you, Peter! I think I should put more detailed information here. What I'm doing is piRNA data. Two groups of piRNA (named sense and antisense)are in the library. As I said, they are complementary to each other for about 10 nt, while the whole length is about 30nt. For the sense group, they share the feature of having an A at their 10th. In this case, how can I deal with it? One possible way come up is inverting all sequences and aligning them. Thanks! Best, Zhiqiang Quoting Peter Cock p.j.a.c...@googlemail.com: On Mon, Nov 26, 2012 at 6:47 PM, Zhiqiang Shu z...@bio.fsu.edu wrote: Hi, Galaxy users! I have a question on how to find out sense and antisense sequence. I've got RNA seq data in the fastq format. The sequences inside are partially complementary to each other (complementary is 10nt, while entire is about 30nt). How can I separate these sequences into two groups: sense and antisense Depending on how your sequences were prepared, you might be able to look for a poly-A tail as a clue to orientation. Another approach is to compare the (assembled) transcripts to known genes and if you only get matches on one strand that is probably the correct orientation. (one thing I know is for the sense sequence the 10th nucleotide is always A)? Why is that? Is this related to your library preparation? Peter -- Zhiqiang Shu/Deng Lab Department of Biological Science Florida State University 319 Stadium Dr. Tallahassee, FL, USA, 32306-4295 z...@bio.fsu.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] Find out sense and antisense sequences
When do you need them and are you likely to need more in the future? We used the TruSeq whole exome kits, though we plan to switch to Agilent. Currently using Agilent's Kinome kit, would have them available. Agilent give substantial volume discount Richard B. Everson, MD, MPH Deputy Director for Cancer Prevention and Control Carole and Ray Neag Comprehensive Cancer Center University of Connecticut Health Center 263 Farmington Ave MC 1628 Farmington, Connecticut 06030-2875 email: ever...@uchc.edu Phone: (860) 679-6055 Fax: Pt (860) 679-4815 Admin (860) 679-4451 -Original Message- From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Zhiqiang Shu Sent: Monday, November 26, 2012 3:29 PM To: Peter Cock Cc: Galaxy-user Subject: Re: [galaxy-user] Find out sense and antisense sequences Thank you, Peter! I think I should put more detailed information here. What I'm doing is piRNA data. Two groups of piRNA (named sense and antisense)are in the library. As I said, they are complementary to each other for about 10 nt, while the whole length is about 30nt. For the sense group, they share the feature of having an A at their 10th. In this case, how can I deal with it? One possible way come up is inverting all sequences and aligning them. Thanks! Best, Zhiqiang Quoting Peter Cock p.j.a.c...@googlemail.com: On Mon, Nov 26, 2012 at 6:47 PM, Zhiqiang Shu z...@bio.fsu.edu wrote: Hi, Galaxy users! I have a question on how to find out sense and antisense sequence. I've got RNA seq data in the fastq format. The sequences inside are partially complementary to each other (complementary is 10nt, while entire is about 30nt). How can I separate these sequences into two groups: sense and antisense Depending on how your sequences were prepared, you might be able to look for a poly-A tail as a clue to orientation. Another approach is to compare the (assembled) transcripts to known genes and if you only get matches on one strand that is probably the correct orientation. (one thing I know is for the sense sequence the 10th nucleotide is always A)? Why is that? Is this related to your library preparation? Peter -- Zhiqiang Shu/Deng Lab Department of Biological Science Florida State University 319 Stadium Dr. Tallahassee, FL, USA, 32306-4295 z...@bio.fsu.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/ ___ 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/
