Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • update on bisulfite mapping program: BSMAP-2.4

    This is an announcement of the release of BSMAP v2.4, a powerful bisulfite mapping program. This version improved a lot on the run time performance, while maintaining high accuracy and flexibility of previous versions.

    Using 8 threads, BSMAP-2.4 can map 28M 76nt pair-end WGBS reads to the human genome in about 2 hours (allow up to 6 mismatches), including the genome indexing time. The memory usage is ~9GB. (CPU: Intel Xeon X5690)

    We tested the mapping accuracy using simulated bisulfite reads. BSMAP have significantly higher mapping accuracy than most other bisulfite mapping programs, especially for reads with more than 3 mismatches.

    BSMAP is freely available at http://code.google.com/p/bsmap/

    Main features of BSMAP-2.4:

    1. Reads are directly mapped to original reference genome sequence, no need to preprocess the reads and reference genome to convert C to T.

    2. Support both whole genome bisulfite sequencing (WGBS) mode and reduced representation bisulfite sequencing (RRBS) mode. In RRBS mode, reads are guaranteed to be mapped to digestion sites to increase accuracy. The digestion site information can be also changed to support different digestion enzymes.

    3. Support both "Lister protocol" (sequence 2 forward strands only) and "Cokus protocol" (sequence all 4 bisulfite converted strands)

    4. Support trimming adapter sequences and low quality nucleotides from 3'end of reads

    5. Allow trade off between speed/memory usage/mapping sensitivity. For human genome, the RRBS mode uses ~3GB. In WGBS mode, the typical memory usage is ~9GB, but can be as low as 5GB.

    6. Allow alignment for other nucleotide transitions, for example, can be set to detect the A=>I(G) transition in RNA editing.

    7. Include down stream script to extract methylation ratios from mapping results.

    8. Fasta/Fastq/SAM format input, text/SAM output. single/pair-end mapping. read length up to 144nt, max 15 mismatches allowed.




    We encourage you try this new version for short bisulfite reads mapping.
    Any comments/suggestions/bug reports will be appreciated.

    Thank you,

    Yuanxin Xi

  • #2
    Dear Xi,
    here I have a problem in installation of BSMAP, my system is opensuse 12.3 x86_64 GNU/Linux. and when I make the software, the errors:
    xiao@localhost:~/Software/bsmap-2.74> make
    g++ -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 -c param.cpp -o param.o
    param.cpp: In constructor ‘Param::Param()’:
    param.cpp:8:20: error: ‘_SC_NPROCESSORS_ONLN’ was not declared in this scope
    param.cpp:8:40: error: ‘sysconf’ was not declared in this scope
    make: *** [param.o] Error 1

    could you tell me what I should do to resolve such a error.

    Thank you.

    Xiao

    Comment


    • #3
      adding "#include<unistd.h>" in the beginning of param.cpp would solve this problem.

      Comment


      • #4
        OKay, thank you!

        Comment


        • #5
          Dear Xi

          i used BSmap for mapping and it gave better mapping efficiency as compared to other tools. But there is problem to extract methylation information from .txt file.
          plz suggest to solve it

          Comment

          Latest Articles

          Collapse

          • seqadmin
            The Impact of AI in Genomic Medicine
            by seqadmin



            Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
            02-26-2024, 02:07 PM
          • seqadmin
            Multiomics Techniques Advancing Disease Research
            by seqadmin


            New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

            A major leap in the field has
            ...
            02-08-2024, 06:33 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 02-28-2024, 06:12 AM
          0 responses
          21 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-23-2024, 04:11 PM
          0 responses
          69 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-21-2024, 08:52 AM
          0 responses
          77 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-20-2024, 08:57 AM
          0 responses
          67 views
          0 likes
          Last Post seqadmin  
          Working...
          X