Re: [galaxy-user] Simulating sequencing and removing redundant sequences
Hi Daniel, You would have multiple names for each sequence and that would be quite hard to display. I am sure someone thought through this. Since the sequence is the same, you can use the sequence to look back in the fastq file for read name. Although I am not sure how that would help you? Cheers Kevin On 20 September 2011 13:43, Daniel Sher ds...@sci.haifa.ac.il wrote: Thanks Kevin. However, the collapse sequences replaces the original name of the sequences with a numerical code, and I need to keep the original names. Any other suggestions? Thanks Daniel On 20/09/2011 05:32, Kevin Lam wrote: Hi Daniel for 2) you may use the tools under NGS QC and manipulation FASTQ to FASTAhttp://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastq_to_fastaconverter followed by Collapsehttp://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastx_collapsersequences On 19 September 2011 09:54, Kevin Lam ke...@aitbiotech.com wrote: For 1) you may refer to Simulated Dataset of Solexa - SEQanswershttp://seqanswers.com/forums/showthread.php?t=806 Has anyone replied you for 2) ? On 18 September 2011 21:12, Daniel Sher ds...@sci.haifa.ac.il wrote: Hello, I have two questions - I apologize if they are trivial.. 1) I want to simulate the amount of Illumina sequencing needed to sequence and assemble a known genome. Is there a way to randomly pick sequences of a specific length from a genome (either one available online or one I upload)? Something like pick 100bp randomly (either strand), move 400-500bp forward and pick another 100bp? 2) Is there a way to remove redundant sequences from a FASTA file without losing the original sequence names (as happens with collapse)? Thanks Daniel -- ~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel Office +972-4-8240731 Lab+972-4-8288961 email: ds...@sci.haifa.ac.il ___ 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/ -- ~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel Office +972-4-8240731 Lab+972-4-8288961 email: ds...@sci.haifa.ac.il ___ 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] Simulating sequencing and removing redundant sequences
For read simulation, you may also want to give Grinder a try. I made a Galaxy wrapper for it (see in the toolshed: http://toolshed.g2.bx.psu.edu/) Florent On 20/09/11 18:46, Kevin Lam wrote: Hi Daniel, You would have multiple names for each sequence and that would be quite hard to display. I am sure someone thought through this. Since the sequence is the same, you can use the sequence to look back in the fastq file for read name. Although I am not sure how that would help you? Cheers Kevin On 20 September 2011 13:43, Daniel Sher ds...@sci.haifa.ac.il mailto:ds...@sci.haifa.ac.il wrote: Thanks Kevin. However, the collapse sequences replaces the original name of the sequences with a numerical code, and I need to keep the original names. Any other suggestions? Thanks Daniel On 20/09/2011 05:32, Kevin Lam wrote: Hi Daniel for 2) you may use the tools under NGS QC and manipulation FASTQ to FASTA http://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastq_to_fasta converter followed by Collapse http://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastx_collapser sequences On 19 September 2011 09:54, Kevin Lam ke...@aitbiotech.com mailto:ke...@aitbiotech.com wrote: For 1) you may refer to Simulated Dataset of Solexa - SEQanswers http://seqanswers.com/forums/showthread.php?t=806 Has anyone replied you for 2) ? On 18 September 2011 21:12, Daniel Sher ds...@sci.haifa.ac.il mailto:ds...@sci.haifa.ac.il wrote: Hello, I have two questions - I apologize if they are trivial.. 1) I want to simulate the amount of Illumina sequencing needed to sequence and assemble a known genome. Is there a way to randomly pick sequences of a specific length from a genome (either one available online or one I upload)? Something like pick 100bp randomly (either strand), move 400-500bp forward and pick another 100bp? 2) Is there a way to remove redundant sequences from a FASTA file without losing the original sequence names (as happens with collapse)? Thanks Daniel -- ~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel Office+972-4-8240731 tel:%2B972-4-8240731 Lab+972-4-8288961 tel:%2B972-4-8288961 email:ds...@sci.haifa.ac.il mailto:ds...@sci.haifa.ac.il ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ -- ~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel Office+972-4-8240731 tel:%2B972-4-8240731 Lab+972-4-8288961 tel:%2B972-4-8288961 email:ds...@sci.haifa.ac.il mailto:ds...@sci.haifa.ac.il ___ 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/
[galaxy-user] Simulating sequencing and removing redundant sequences
Hello, I have two questions - I apologize if they are trivial.. 1) I want to simulate the amount of Illumina sequencing needed to sequence and assemble a known genome. Is there a way to randomly pick sequences of a specific length from a genome (either one available online or one I upload)? Something like "pick 100bp randomly (either strand), move 400-500bp forward and pick another 100bp?" 2) Is there a way to remove redundant sequences from a FASTA file without losing the original sequence names (as happens with "collapse")? Thanks Daniel -- ~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel Office +972-4-8240731 Lab+972-4-8288961 email: ds...@sci.haifa.ac.il ___ 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] Simulating sequencing and removing redundant sequences
For 1) you may refer to Simulated Dataset of Solexa - SEQanswershttp://seqanswers.com/forums/showthread.php?t=806 Has anyone replied you for 2) ? On 18 September 2011 21:12, Daniel Sher ds...@sci.haifa.ac.il wrote: Hello, I have two questions - I apologize if they are trivial.. 1) I want to simulate the amount of Illumina sequencing needed to sequence and assemble a known genome. Is there a way to randomly pick sequences of a specific length from a genome (either one available online or one I upload)? Something like pick 100bp randomly (either strand), move 400-500bp forward and pick another 100bp? 2) Is there a way to remove redundant sequences from a FASTA file without losing the original sequence names (as happens with collapse)? Thanks Daniel -- ~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel Office +972-4-8240731 Lab+972-4-8288961 email: ds...@sci.haifa.ac.il ___ 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/
