Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie2 and MapQ Calculation

    Hi

    I'm going to ask about bowtie2's mapping quality calculation for ChIP-Seq data. For sequences which align multiple locations Bowtie2 gives the MAPQ 30. It says for multiple aligned sequences, mapq is not meaningful, so why it gives 30 for all? Other thing it gives 30 for completely aligned sequence and sequences which has indels too. What is that 30 and why?

    I attached a png file about my ask.
    Attached Files
    Last edited by KyuzoSeq; 03-08-2015, 05:47 AM.

  • #2
    Outline: I. Introduction II. A little bit to know about bowtie2     A. How bowtie2 scores a mismatch     B. How bowtie2 deci...


    Here is added discussion on biostars: https://www.biostars.org/p/110958/

    Comment


    • #3
      Chip-seq mappers

      Hello Geno Max and all,

      I am inquiring about Chip-seq mapping software. I am using the Arabidopsis TAIR10 genome as a reference.

      I have used for RNA-seq tophat2 to account for splicing, which is something we are not really concerned when doing Chip-seq (right ?).

      I have read that people uses Bowtie, and SOAP, SOAP2 when mapping against TAIR10. Before i get my Illumina reads, I'd like to know if you have an idea as to which mapper would be best?

      Many thanks in advance.

      Cheers

      G
      Last edited by Gonza; 11-02-2015, 10:01 AM.

      Comment


      • #4
        @Gonza: You could use any modern aligner for the alignment. You don't need to worry about splicing with ChIP-seq. I like @blancha's advice in a recent thread. Pick an aligner and become familiar with its myriad options (most have many) rather than hopping from one aligner to next.

        Comment


        • #5
          Hi GenoMax

          I am mapping Illumina reads to a indexed genome with soap Version: 2.21 http://soap.genomics.org.cn/soapaligner.html

          It seems to work fine, the only problem is that i cannot find the % of mapped reads. I am used to tophat that tells you % of mapped/unmapped. Is there a way to see % of mapped reads when using soap?

          Script:
          $soap -r 0 -M 1 -a sample1.fq -D genome.fa.index -o SOAP.sample1

          Thanks

          Comment


          • #6
            @Gonza: I am not familiar with soap but have you looked to see if soap writes any log files? Those may contain the information you are looking for.

            Otherwise you could use "samtools idxstats" command or a package like Qualimap to find this information.

            Comment


            • #7
              thanks, will look into Qualimap

              Comment

              Latest Articles

              Collapse

              • 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
              • 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

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 03-14-2024, 06:13 AM
              0 responses
              32 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-08-2024, 08:03 AM
              0 responses
              71 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-07-2024, 08:13 AM
              0 responses
              80 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-06-2024, 09:51 AM
              0 responses
              68 views
              0 likes
              Last Post seqadmin  
              Working...
              X