Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • AMOS & BAMBUS program experience sharing and general user guide.

    Hi,

    Anybody willing to share the experience of using AMOS & BAMBUS program?
    Can give the general explanation about this two program and general user guide of these two program?
    Thanks a lot for sharing and advise

  • #2
    HI Patrick,

    Did you get any assistance about AMOS. I am at the same position when you did this post. Any help you can do?
    ~Adnan~

    Comment


    • #3
      Hi,

      I just subscribe with the AMOS help. I learning from there now. What problem you have facing now? Anything I can help you too? Maybe we face the same situation too.

      Comment


      • #4
        i have installed AMOS but i dont know how to make relevant input formats from illumina reads and reference sequence.
        ~Adnan~

        Comment


        • #5
          Adnan,

          AMOS is a pretty large suite of tools, what are you trying to do more specifically, maybe I can share some war stories if I know where to start.
          Justin H. Johnson | Twitter: @BioInfo | LinkedIn: http://bit.ly/LIJHJ | EdgeBio

          Comment


          • #6
            Thanks johnson. I am actually intending to do comparative assembly of bacterial strain whose data is from illumina GA2 with 75bp of reads. The data was in scarf format and i converted it into standard fastq format. Now the thing is that AMOScmp-shortreads takes two inputs .1con and .afg. How to convert reference sequence to .1con? And which steps should i follow till final assembly, viewing and validation? Thanks
            ~Adnan~

            Comment


            • #7
              Also how i convert paired end reads in .afg format since nowhere on AMOS pages is mentioned about paired end reads conversion. I am gone mad in this, no help on the web and at AMOS-help.
              ~Adnan~

              Comment


              • #8
                Hi [email protected],

                Did you find out about this reference file? I can't find much info anywhere about it!

                Thanks,

                Kasycas

                Comment


                • #9
                  I got an error when I make files for Bambus, can anybody give help? Thanks,
                  The error is bellow:

                  for i in src doc ;do cd $i ; make all; cd .. ; done
                  make[1]: Entering directory `/home/ngs/SL/software/bambus-2.33/src'
                  for i in IO DotLib TIGR_Foundation_CC grommit ;do cd $i ; make all; cd .. ; done
                  make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/IO'
                  make[2]: Nothing to be done for `all'.
                  make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/IO'
                  make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/DotLib'
                  make[2]: Nothing to be done for `all'.
                  make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/DotLib'
                  make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/TIGR_Foundation_CC'
                  g++ -D_HAS_GETOPT -c -o ConfigFile.o ConfigFile.cc
                  ConfigFile.cc: In member function ‘void ConfigFile:arseConfig()’:
                  ConfigFile.cc:113: error: ‘strlen’ was not declared in this scope
                  make[2]: *** [ConfigFile.o] Error 1
                  make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/TIGR_Foundation_CC'
                  make[2]: Entering directory `/home/ngs/SL/software/bambus-2.33/src/grommit'
                  g++ -I../TIGR_Foundation_CC/ -g -c grommit.cc
                  grommit.cc: In function ‘int main(int, char**)’:
                  grommit.cc:236: warning: format ‘%s’ expects type ‘char*’, but argument 3 has type ‘char (*)[1024]’
                  grommit.cc:317: error: ‘abort’ was not declared in this scope
                  make[2]: *** [grommit.o] Error 1
                  make[2]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src/grommit'
                  make[1]: Leaving directory `/home/ngs/SL/software/bambus-2.33/src'
                  make[1]: Entering directory `/home/ngs/SL/software/bambus-2.33/doc'
                  make[1]: Nothing to be done for `all'.
                  make[1]: Leaving directory `/home/ngs/SL/software/bambus-2.33/doc'

                  Comment

                  Latest Articles

                  Collapse

                  • seqadmin
                    Strategies for Sequencing Challenging Samples
                    by seqadmin


                    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                    03-22-2024, 06:39 AM
                  • seqadmin
                    Techniques and Challenges in Conservation Genomics
                    by seqadmin



                    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                    Avian Conservation
                    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                    03-08-2024, 10:41 AM

                  ad_right_rmr

                  Collapse

                  News

                  Collapse

                  Topics Statistics Last Post
                  Started by seqadmin, 03-27-2024, 06:37 PM
                  0 responses
                  12 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-27-2024, 06:07 PM
                  0 responses
                  11 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-22-2024, 10:03 AM
                  0 responses
                  53 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-21-2024, 07:32 AM
                  0 responses
                  68 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X