No I believe there isn't sth like that. It should be a simple perl script to get that info or linux grep would help
On 20 September 2011 17:43, Daniel Sher dsher@sci.haifa.ac.il wrote:
Thanks Kevin - that might work - collapse sequences and then grab the sequence names using "select" (under filter and sort tools). Is there a way to "loop" such a search in order to go through the lines of a long file? I assume there must be something in the workflows but I have never used that feature.
Thanks
Daniel
On 20/09/2011 11:46, 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 dsher@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 kevin@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 dsher@sci.haifa.ac.il wrote:
Hello,
I have two questions - I apologize if they are trivial..
- 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?"
- 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: dsher@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: dsher@sci.haifa.ac.il--
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: dsher@sci.haifa.ac.il