Re: [galaxy-user] Simulating sequencing and removing redundant sequences

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 wrote: > Thanks Kevin - that might work - collapse sequences and then grab the > sequence names using "select" (under filter and sort to

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 a

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

Re: [galaxy-user] Simulating sequencing and removing redundant sequences

Hi Daniel for 2) you may use the tools under NGS QC and manipulation FASTQ to FASTAconverter followed by Collapsesequences On 19 September 2011 09:54, Kevin

Re: [galaxy-user] Simulating sequencing and removing redundant sequences

For 1) you may refer to Simulated Dataset of Solexa - SEQanswers Has anyone replied you for 2) ? On 18 September 2011 21:12, Daniel Sher wrote: > Hello, > > I have two questions - I apologize if they are trivial.. > > 1) I want to simulate