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  • Hi from France

    Hello everybody,

    I'm from Lille, North of France. I work on NGS since 1 month only, but I hope for a long time.

    Thanks for this very useful forum.

    Comment


    • dear friends
      I am new member for NGS analysis and have the following data. any help would be appreciated from the members or the administrator of the group
      1. i am working on mus musculus and in building the indexes, bowtie takes a long time, more than 2 days for all the chromosomes. instead of building the indexes together, which takes a long time for buffering, can i build it one by one?. it takes hardly 25 mins for a single chromosome indexing and hence one can build the indexes for all the chromosomes within 500 mins or less than 10 hrs. pls reply

      with regards
      Sr. Application Scientist, Apsara Innovations, Bangalore
      E-Mail: [email protected]

      Comment


      • Hi to all

        I am a doctoral student, assembling partial fosmid libraries and organellar genome from the plant family Zingiberaceae.

        Comment


        • Hi everybody
          I am a virology graduate student, preparing to do a whole genome sequence project using 454.
          Good luck!

          Comment


          • Hi everyone!

            Mathematics and statistics. Recently (2009) switched to applications in biology and genetics. What a mess we got here!

            University of Warsaw (Poland), Georgia Health Sciences University (USA), Florida State University (USA).
            Sergiusz Wesolowski

            Comment


            • Concatenating vcf files

              Hi y'all. I'm a retired old guy who spent his whole life wishing that genomics would come along, now it's here and I'm almost too old. But I have some data, a linux system, and some software running, and many problems/questions. Like the oldest dumbest grad student you ever hear of. Very gald to find this site.
              Current question is how to concatenate vcf files for individual chromosomes into a single genome. Have been running vcf-concat (from vcf tools) but no matter what I try, get the same error messages.

              The column names do not agree in [../Chrm2/Chrm2.vcf].
              at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 32
              main::error('The column names do not agree in [../Chrm2/Chrm2.vcf].\x{a}') called at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 114
              main::concat('HASH(0x21cf518)') called at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 12

              Yet as near as I can tell, the two .vcf files have exactly the same columns, nice illumina data, looks clean, something just not right. Thanks

              Comment


              • Hi, I am ZHAO, Guangzhou ,China. a student of bioinfromatics engaging in biosoftware developing by Java. recently ,I just focus on RNA-seq data analysis. glad to be here!

                Comment


                • Tahir Mujtaba

                  Hi, I am Tahir from Sweden and i am new to Bioinformatics, i need some help/gudieline to use BOWTIE,TOPHAT,CUFFLINKS, etc, can we negotiate further at ([email protected]).
                  Originally posted by olus View Post
                  Hi everibody.
                  My name is Gabriel, I'm a biologist and bioinformatician. I'm currently working in the core facility of a Molecular Oncology research campus in Milan (italy).
                  We are using Illumina Genome Analyzer II mainly for ChIP-Seq, but we've already done a resequencing and some RNA-seq are approaching ;-)

                  Comment


                  • Hello, do you know BOWTIE?,Can you help me learning this tool, i am new to Bioinformatics.
                    Originally posted by rathankar View Post
                    dear friends
                    I am new member for NGS analysis and have the following data. any help would be appreciated from the members or the administrator of the group
                    1. i am working on mus musculus and in building the indexes, bowtie takes a long time, more than 2 days for all the chromosomes. instead of building the indexes together, which takes a long time for buffering, can i build it one by one?. it takes hardly 25 mins for a single chromosome indexing and hence one can build the indexes for all the chromosomes within 500 mins or less than 10 hrs. pls reply

                    with regards

                    Comment


                    • Dear All,

                      I am new to the sequencing world and have just managed to install SSAKE and VELVET.
                      Kindly, tell of how to use them.

                      Regards

                      Comment


                      • Hi,

                        I am Maude, a phD student in Belgium.
                        I work on the alternative splicing on the transcriptome using genome analyser (illlumina)

                        Greetings!

                        Comment


                        • Hi !
                          I am a new bird in next generation seq and data analysis. I am trying to establish the ChIP-seq tech in our lab. I am glad to meet you all here. Thanks for all the helps.

                          I am a PhD student in the University of Florida, working on cancer metastasis and tumor angiogenesis.

                          Comment


                          • hello everyone

                            i am a bioinformatics masters student workking on my project at ohio state still getting the hang of working and anlysing RNA-seq data

                            Comment


                            • Hi,

                              My name is Haiyan, a fellow in FDA. We try to identify the new pathogen from the human samples. We will use the Illumina miseq platform. Thanks.

                              haiyan

                              Comment

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