Menu
▾
▴
Re: [Ergatis-users] Next generation sequencing - analysis with ergatis
|
From: Chris H. <che...@cg...> - 2010-05-03 17:41:55
|
Gowthaman, I got the go ahead to proceed with this at our meeting. There is a definite question on how consistent the time we can commit to this will be, so maybe we can work together to prioritize some components and then each tackle one at a time, so we aren't locking more than we are currently working on. I can set up a temporary mailing list for discussing priorities and which particular programs to implement. Another alternative would be to carve out some wiki space somewhere. Chris On Mon, 26 Apr 2010, Gowthaman Ramasamy wrote: > HI Chris, > The story is pretty much same here. When we get some new data, we generate cluster ready shell scripts for each step, which then will be invoked by the the scientist who generated the data. It will be very interesting to run these via ergatis. Esp, with support coming for ez2 clusters. Please let us know. Plus, I'm interested to see what Anup has in place already. > > To be added to the list... > 12) support for some chip-seq package > > Thanks. > Gowtham > > > On 4/26/10 9:09 AM, "Chris Hemmerich" <che...@cg...> wrote: > > > > Gowtham, > > > I've talked with some of the people here, and we are interested in all of > these points - running about half by hand now, and evaluating programs for > the other half. We will discuss this at our group meeting on Wednesday > and figure out how much time we can contribute. > > Thanks, > > Chris > > > On Thu, 22 Apr 2010, Gowthaman Ramasamy wrote: > >> Hi Chris, Anup and others, >> I am sorry for the delay in replying. >> >> Of course, there are lot of tools out there to implement. I just made a list based on what we use at Seattle BioMed. The list is not exhaustive neither points to a specific utility. Feel free to edit, comment on the points. Once we make a high priority list and compare them against the components made at IGS we can split the work. Also, it will be very useful to settle on our software preferences (bowtie over maq etc). But, I guess, once we have components for one software, it will be trivial to modify it for a similar one. >> >> >> 0) Quality analyzes of the raw reads (like the one in Galaxy) >> 1) Filtering reads based on some motifs/tags at particular position >> 2) Align reads using bowtie (& other) against ref. >> 3) converting one format to another (e.g., bowtie to sam) >> 4) Implementing SAMtools to facilitate many format conversions (SAM->BAM->sorted BAM -> indexed BAM etc) >> 5) Implementing some of the HTseq utilities etc... >> 6) assembling reads into contigs (de nova and ref. based) >> 7) ordering, orienting assembled contigs into chromosomes based on a reference genome >> 8) Calculating coverage and other statistics >> 9) Making different output files to view the results in different viewers....eg, bed, wig, gff etc... >> 10) Expression analyzes and differential expression analyzes utilities (eg DEseq, cufflinks) >> 11) implementing SNP callers etc..... >> >> Anup, will it be possible for us to get a handle on what components IGS has already. >> Thanks very much, >> >> ________________________________________ >> From: Gowthaman Ramasamy [gow...@se...] >> Sent: Thursday, April 15, 2010 10:21 AM >> To: erg...@li... >> Subject: Re: [Ergatis-users] Next generation sequencing - analysis with ergatis >> >> Hi Chris, >> That is lovely. In couple days, I will make a list of what are my needs/plans. Then we can split the work. I have developed couple components for eragtis earlier. >> >> Meanwhile, Anup mentioned, they have couple of them made already. I assume they have all the basic ones. So, we can work with him to finalize what we need to do. >> But, with a quick look at ergatis SVN (http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/components/), I don't see any component for NGS analysis. I guess, they are still under development. >> >> Gowtham >> ________________________________________ >> From: Chris Hemmerich [che...@cg...] >> Sent: Wednesday, April 14, 2010 8:45 PM >> To: erg...@li... >> Subject: Re: [Ergatis-users] Next generation sequencing - analysis with ergatis >> >> Gowtham, >> >> We are also analyzing NGS data (454 and Illumina), and looking into >> migrating some of that code to our Ergatis installation. It doesn't sound >> like we are any further ahead than you are, but we have experience >> developing Ergatis components and would be interested in comparing notes >> to see if we can split the work. >> >> Chris >> >> >> On Tue, 13 Apr 2010, Gowthaman Ramasamy wrote: >> >>> Hi Everyone, >> >>> Here at Seattle Biomed we generate and analyze NGS data (as every lab >>> around the corner). We currently use collection of shell scripts, perl/R >>> scripts and some packages. We would love make components for them at >>> ergatis/WF. >>> >>> But, I am writing this to check if some one else has done this already >>> (atleast some components). ANd if yes, would you like to share it with >>> others. So that I don;t duplicate the efforts. >>> >>> Thanks everyone, >>> gowtham >>> ________________________________________ >>> >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® Parallel Studio Eval >>> Try the new software tools for yourself. Speed compiling, find bugs >>> proactively, and fine-tune applications for parallel performance. >>> See why Intel Parallel Studio got high marks during beta. >>> http://p.sf.net/sfu/intel-sw-dev >>> _______________________________________________ >>> Ergatis-users mailing list >>> Erg...@li... >>> https://lists.sourceforge.net/lists/listinfo/ergatis-users >>> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> Ergatis-users mailing list >> Erg...@li... >> https://lists.sourceforge.net/lists/listinfo/ergatis-users >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> Ergatis-users mailing list >> Erg...@li... >> https://lists.sourceforge.net/lists/listinfo/ergatis-users >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> Ergatis-users mailing list >> Erg...@li... >> https://lists.sourceforge.net/lists/listinfo/ergatis-users >> > > ------------------------------------------------------------------------------ > _______________________________________________ > Ergatis-users mailing list > Erg...@li... > https://lists.sourceforge.net/lists/listinfo/ergatis-users > > |