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  • #61
    Besides for the base just the same as reference base. The variant is which has the largest frequency.

    Originally posted by Drake View Post
    Hello again,
    Can anyone explain me how the 'VariantFrequency' in the stat file is calculated?
    I mean, it's obvious how the frequency is calculated for one variant base. But how is it done for two or three variant bases?
    I also attached an excerpt from my stat file. Row 369 and 370 are clear to me, but would anyone be so kind to explain me the other two?

    Thanks in advance!

    Comment


    • #62
      The SNP detection will look at each position in the contig to determine if there is a SNP at this position. In order to make a qualified and significant assessment, it needs three thresholds:

      (1). Minimum quality of central base. Bases with a quality score below this value are not considered in the SNP calculation at this position.

      (2). Minimum coverage. If SNPs were called in areas of low coverage, you would get a higher amount of false positives. Therefore you can set the minimum coverage for a SNP to be called. Note that the coverage is counted as the number of valid reads at the current position (i.e. the reads remaining when the quality assessment has filtered out the bad ones).

      (3). Minimum variant frequency. If only one read has a variant base, you probably do not want this to count as a SNP. This threshold is used to determine the minimum frequency for a variant to be called a SNP. Per default, the value is set to 0.4, which means that there should be a variant base in at least 40% of the bases in the valid reads before a SNP is called. Note that if you have two different variants with each having e.g. 20% frequency, it will not be counted as a SNP. If you sequence diploid genomes, you may have to lower this value to detect all SNPs.

      Comment


      • #63
        Originally posted by baohua100 View Post
        The SNP detection will look at each position in the contig to determine if there is a SNP at this position. In order to make a qualified and significant assessment, it needs three thresholds:

        (1). Minimum quality of central base. Bases with a quality score below this value are not considered in the SNP calculation at this position.

        (2). Minimum coverage. If SNPs were called in areas of low coverage, you would get a higher amount of false positives. Therefore you can set the minimum coverage for a SNP to be called. Note that the coverage is counted as the number of valid reads at the current position (i.e. the reads remaining when the quality assessment has filtered out the bad ones).

        (3). Minimum variant frequency. If only one read has a variant base, you probably do not want this to count as a SNP. This threshold is used to determine the minimum frequency for a variant to be called a SNP. Per default, the value is set to 0.4, which means that there should be a variant base in at least 40% of the bases in the valid reads before a SNP is called. Note that if you have two different variants with each having e.g. 20% frequency, it will not be counted as a SNP. If you sequence diploid genomes, you may have to lower this value to detect all SNPs.
        Thanks a lot for your explanation! ... This is pretty much the same as MAQ does .. and I'm familiar with that.

        My question was rather how the 'variant frequency' is calculated?
        Referring to my attached picture:
        Row 370 does not have any variant base - so the percentage is zero.
        Row 369 has one variant base - so the percentage is 2 / 53 = 3.77%
        ...
        But how are 368 and 371 calculated?

        Thanks!

        Comment


        • #64
          X= The number of variant base with largest frequency
          Y= The number of the nucletide the same as reference base

          variant frequency= X/(X+Y)

          reference : T

          A: 30 T:60 G:10 C:5

          X= 30, Y=60 variant frequency=0.333


          reference: T

          A: 60 T:60 G:10 C:5

          X=60, Y=60 variant frequency=0.5


          Originally posted by Drake View Post
          Thanks a lot for your explanation! ... This is pretty much the same as MAQ does .. and I'm familiar with that.

          My question was rather how the 'variant frequency' is calculated?
          Referring to my attached picture:
          Row 370 does not have any variant base - so the percentage is zero.
          Row 369 has one variant base - so the percentage is 2 / 53 = 3.77%
          ...
          But how are 368 and 371 calculated?

          Thanks!

          Comment


          • #65
            Thanks a lot! I really appreciate!

            Comment


            • #66
              Can Mapview visualize Bowtie alignment? I tried using the user defined format it did not work

              Comment


              • #67
                You should specify the following items according to Bowtie output format:

                R: Read ID
                A: Read seq
                Q: Quality score(maybe x)
                C: Chromosome
                P: Mapping Position
                S: Strand(F/R or +/-)
                x: (neglected / pass over)


                For example:
                SOAP output:

                8:1:3:1697 GTCTAGATATCGCACAATCTTNAATCTTTAAAATG hhhhhhhhhhhhhhhhhhhhh;hhhhhhhhhhhhh 1 a 35 - chr1 1266 0


                So the corresponding format:

                R A Q x x x S C P <User-defiend> 1 0


                Sort 1 means the alignment position is not sorted. So MapView will sort.
                Reverse 1 means the read sequence (-) must be complementary reverse when display.

                Comment


                • #68
                  Thanks. I wonder if I can combine visualize 2 lanes in the same time. I have input and control and I do the splitter for each of the input and control. Can I visualize both of them in the same time

                  Comment


                  • #69
                    Hi,
                    I tried to use mapview with linux (using mono, of course) but I obtained this error:

                    Code:
                    Unhandled Exception: System.ComponentModel.Win32Exception: Access denied
                      at System.Diagnostics.Process.set_PriorityClass (ProcessPriorityClass value) [0x00000] 
                      at (wrapper remoting-invoke-with-check) System.Diagnostics.Process:set_PriorityClass (System.Diagnostics.ProcessPriorityClass)
                      at 5k3wLwQTgnplU7ERSH.OBxZknnHvaWwL3tHML.395cY3App () [0x00000]
                    If I try with root (using "sudo") the program works.

                    The problem is that the program try to gain priority than the other process. On linux systems this is not possibile for normal users.

                    I need to allow other users (that can not be administrators) to use the program under linux (we do not use windows). It is possibile to solve the problem (for example adding a command line parameter or checking the operating system)?

                    Thank you very much
                    Cristian

                    Comment


                    • #70
                      Originally posted by cdf View Post
                      Hi,
                      I tried to use mapview with linux (using mono, of course) but I obtained this error:

                      Code:
                      Unhandled Exception: System.ComponentModel.Win32Exception: Access denied
                        at System.Diagnostics.Process.set_PriorityClass (ProcessPriorityClass value) [0x00000] 
                        at (wrapper remoting-invoke-with-check) System.Diagnostics.Process:set_PriorityClass (System.Diagnostics.ProcessPriorityClass)
                        at 5k3wLwQTgnplU7ERSH.OBxZknnHvaWwL3tHML.395cY3App () [0x00000]
                      If I try with root (using "sudo") the program works.

                      The problem is that the program try to gain priority than the other process. On linux systems this is not possibile for normal users.

                      I need to allow other users (that can not be administrators) to use the program under linux (we do not use windows). It is possibile to solve the problem (for example adding a command line parameter or checking the operating system)?

                      Thank you very much
                      Cristian
                      Hi,Cristian

                      Thank you for your message.

                      I will add a command line parameter to change the process priority.

                      WJW-Davy
                      WJW-Davy
                      HomePage: http://hi.baidu.com/wjwdavy
                      Download Center: https://sites.google.com/site/wjwdavy/

                      Comment


                      • #71
                        Originally posted by WJW-Davy View Post
                        Hi,Cristian

                        Thank you for your message.

                        I will add a command line parameter to change the process priority.

                        WJW-Davy
                        Fast answer, great! :-D

                        I must wait for a new version on the main site or can you give me a patched file to test it?

                        Many thanks,
                        Cristian

                        Comment


                        • #72
                          Originally posted by cdf View Post
                          Fast answer, great! :-D

                          I must wait for a new version on the main site or can you give me a patched file to test it?

                          Many thanks,
                          Cristian
                          Hi,Cristian
                          After replying that post, I went to make some changes about MapView. Sorry for not noticing your lastest post.
                          Thank you very much for testing MapView on Linux.
                          Here is the beta version :
                          Access Google Sites with a personal Google account or Google Workspace account (for business use).


                          added a command line parameter "-high".
                          MapView's default ProcessPriority is Normal.
                          But when start it with parameter:
                          MapView -high
                          MapView will try to gain priority to be high.
                          WJW-Davy
                          HomePage: http://hi.baidu.com/wjwdavy
                          Download Center: https://sites.google.com/site/wjwdavy/

                          Comment


                          • #73
                            Originally posted by iaaa99 View Post
                            Thanks. I wonder if I can combine visualize 2 lanes in the same time. I have input and control and I do the splitter for each of the input and control. Can I visualize both of them in the same time
                            You should combine the alignment output files fisrt. Then you can make MVF file.

                            Comment


                            • #74
                              Run Mapview on Linux (Ubuntu) using Mono. Its' fine!

                              Comment


                              • #75
                                Special thanks to Cristian!
                                MapView 3.4.0 Beta3 is running on Linux (Ubuntu 9.04) successfully.
                                After some changes and tests, I will release MapView 3.4.0 asap.
                                WJW-Davy
                                HomePage: http://hi.baidu.com/wjwdavy
                                Download Center: https://sites.google.com/site/wjwdavy/

                                Comment

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