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  • Consed is very similar to gap4 and now assembles illumina short reads.

    I have been happy with the assembly to a reference sequence & the contig viewer & searching for highly discrepant regions.

    hope this is of help

    alig

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    • CNV-seq

      a package to detect DNA copy number variation using shotgun sequencing.

      Background DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. Results Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. Conclusion Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes.

      Comment


      • MapView: a short reads alignment viewer with genetic variation analysis, visualization of short reads alignment on desktop computer

        http://evolution.sysu.edu.cn/mapview/
        WJW-Davy
        HomePage: http://hi.baidu.com/wjwdavy
        Download Center: https://sites.google.com/site/wjwdavy/

        Comment


        • Originally posted by kopi-o View Post
          I didn't see MACS and PeakSeq among the ChIP-seq peak callers. Those should be added.
          Seconded. MACS is a useful tool.

          Comment


          • Originally posted by RudyS View Post
            thanks swbarnes2

            i think i will post a query on the UCSC listserver
            [email protected]
            and see if someone like Jim Kent is thinking about some utility that could facilitate reference assembly on a local Genome Browser ... he's the guy i think who initiated BLAT and isPCR on their site



            the browser can be installed locally and used with any genome ... but without taking into account quality values from the reads its hard to imagine not getting just a mess doing a BLAT-like alignment ... i think

            RudyS
            Is there anybody have the experience to install UCSC locally with other genome database like arabidopsis? I hope I can find a detailed procedure to set it locally.
            Thanks!

            Comment


            • xuer
              the browser is well documented ... suggest you write to the nice folks on the listserver there

              [email protected]

              Rudy

              Comment


              • Meeting in Berlin this month

                Xuer, you might also access TAIR scientists who will be attending the International Biocuration Conference in Berlin later this month.
                Die EML European Media Laboratory GmbH ist ein Unternehmen, das forschungsnahe IT-Dienstleistungen von der Auftragsforschung über die Entwicklung innovativer IT-Lösungen bis hin zu Beratung und Schulung anbietet. Im Zentrum unserer Arbeit steht der Mensch: IT-Systeme sollen so entworfen und realisiert werden, dass ihre Benutzer sie als hilfreiche Erweiterungen ihrer eigenen Fähigkeiten erleben und nicht als technische Barrieren.

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                • RudyS,Thank you for the reply.for me the Installation if UCSC is finished, next i need to set the arabidopsis assembly. hopefully it goes well.

                  Joann, Thank you for the information.The topics are interesting , i hope i could be there.

                  Comment


                  • How about Genomatix?

                    Hate to be so blatantly commercial, but in the "not for free" category, you should add Genomatix. No sales pitch here...but check out the vendor forum! Complete analysis capabilities for all current platforms...thanks.

                    Comment


                    • Release V2.03.12 of Novoalign is out. This release improves performance especially for longer reads and is a 4-5 times faster on 45bp reads against Human. Longer reads have improved even more. Performance improvement is more pronounced when allowing more mismatches (higher thresholds).

                      It also seems our web site has been blocked in China so if any one in China wants a copy of novoalign please email me at colin at novocraft dot com. I'll create a mailing list and keep you informed of any updates etc.

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                      • I think it will be a good idea to include RNA-SEQ tools in the huge table. The one tool I know for that = erange
                        --
                        bioinfosm

                        Comment


                        • Any more ChIP-seq analysis tools that we should add here?

                          Also, does anyone know if the program from the Poisson mixture method paper is publicly available?:
                          http://www.biomedcentral.com/1471-2164/9/S2/S23

                          Or if anything has been published about the ChIP-seq Analysis server?
                          http://ccg.vital-it.ch/chipseq/

                          Comment


                          • Originally posted by ewilbanks View Post
                            Any more ChIP-seq analysis tools that we should add here?
                            The Bioconductor 'chipseq' package / programs should be added for sure! See also the other thread on this topic:

                            Any non-primary sequence heritable modification of genetic material. ChIP-SEQ, DNA methylation (Bisulfite-SEQ), chromatin modifications (methylation, acetylation, etc), non coding RNA.
                            Last edited by dan; 05-09-2009, 02:13 AM. Reason: tidy
                            Homepage: Dan Bolser
                            MetaBase the database of biological databases.

                            Comment


                            • RNA-seq tools?

                              Originally posted by bioinfosm View Post
                              I think it will be a good idea to include RNA-SEQ tools in the huge table. The one tool I know for that = erange
                              I'd like to second the call for including RNA-seq tools, e.g. ERANGE, TOPHAT, G-Mo.R-se... any others??

                              Comment


                              • Originally posted by mbjohnson View Post
                                I'd like to second the call for including RNA-seq tools, e.g. ERANGE, TOPHAT, G-Mo.R-se... any others??
                                Also RSAT

                                Comment

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