Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Tophat's bowtie parameters

    Hi folks,

    I am using tophat in my RNA-seq of a high polymorphic genome. I think Tophat calls bowtie with '-v 2', but I found many reads with more than 2 mismatches were mapped to the genome. I took one as the test, it has 5 mismatches with good phred quality scores:

    13:C>T,27:C>A,38:T>C,57:G>A,64:C>A

    Using -v 3, or default -n 2 -l 28 -e 70 cannot map it, but using -n 2 -l 28 -e 150 can map it.

    Why can tophat map these kind of reads?

    Thanks!

  • #2
    I also have a quite similar question: How to set the other bowtie parameters in tophat(such as "-a --best --strata")?

    Comment


    • #3
      Originally posted by Gangcai View Post
      I also have a quite similar question: How to set the other bowtie parameters in tophat(such as "-a --best --strata")?
      I did it just by editing the python script of tophat.
      Xi Wang

      Comment


      • #4
        Originally posted by Xi Wang View Post
        I did it just by editing the python script of tophat.
        How exactly did you do this? Which line and what is the name of the script?

        I appreciate your help in advance. Thanks !

        Comment


        • #5
          you can modify the tophat bin file

          The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

          After modification, you can run tophat like this:

          $tophat --best --strata --seedmms 3 ......

          Originally posted by thinkRNA View Post
          How exactly did you do this? Which line and what is the name of the script?

          I appreciate your help in advance. Thanks !
          Attached Files

          Comment


          • #6
            Originally posted by Gangcai View Post
            The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

            After modification, you can run tophat like this:

            $tophat --best --strata --seedmms 3 ......
            Great! I think tophat developers should also take those options into consideration.
            Xi Wang

            Comment


            • #7
              I agree, one of the strengths of BOWTIE is being able to modify the way it works via its options- but all of this customizability is lost when using TOPHAT..

              Comment


              • #8
                help with Tophat's bowtie parameters

                Originally posted by Gangcai View Post
                The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

                After modification, you can run tophat like this:

                $tophat --best --strata --seedmms 3 ......

                Hi
                If it is not too much trouble, can you post a tophat file with modification to the the latest version (1.2). My data maps better when I set my own -n/--seedmms and -l/--seedlen parameters.
                As you can tell, I don't know how to write scripts.

                Thank you in advance

                Joseph Dhahbi

                Comment


                • #9
                  Originally posted by joseph View Post
                  Hi
                  If it is not too much trouble, can you post a tophat file with modification to the the latest version (1.2). My data maps better when I set my own -n/--seedmms and -l/--seedlen parameters.
                  As you can tell, I don't know how to write scripts.

                  Thank you in advance

                  Joseph Dhahbi
                  I think the authors of Tophat don't want users to run Tophat in this way. One of the reasons should be that those parameters also apply to segment mapping in Tophat. A segment is an arbitrary part of a read, not necessarily from the left end of a read. So the seed region of a segment could be different from the seed of a whole read. This may cause some biases, I guess.
                  Xi Wang

                  Comment


                  • #10
                    TopHat source code modification to include --best

                    Hi all,

                    I want to use TopHat for my mRNA Seq analysis, but I am unable to include --best..

                    I tried modifying the code to include best (similar to what's given above), but I was not successful..

                    Could someone please provide a modification in the latest version (1.3.1)? *I wish tophat did not make it impossible to edit bowtie options on the command line*

                    Comment


                    • #11
                      i have another problem about tophat.
                      i mapped 90bp pair-end reads twice with tophat of different versions with same arguments -g 10 -r 20 --solexa1.3-quals .The default segment-mismatch is 2. in the otput of the older version(1.0.12),the minimum match length is 75bp,why?. in the output of the latest version(1.3.1) it is mostly 90bp, is it because the -v 2 ?
                      is there anyone facing the same problem?

                      Comment


                      • #12
                        Shrutii,
                        U can try a different approach... Might work... If u have already run tophat... there is a log folder in the output directory. Open run.log file. It lists the sequence of commands tophat executes... I think there are 29 steps totally. U can modify the steps in which bowtie is called and give the --best flag... and then run all the commands as a bash script but as Xi Wang mentioned above, I too feel Cole or the other authors of Tophat do not want users to run it this way. I might be wrong tho...

                        Dinesh

                        Originally posted by shrutiisarda View Post
                        Hi all,

                        I want to use TopHat for my mRNA Seq analysis, but I am unable to include --best..

                        I tried modifying the code to include best (similar to what's given above), but I was not successful..

                        Could someone please provide a modification in the latest version (1.3.1)? *I wish tophat did not make it impossible to edit bowtie options on the command line*

                        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
                        14 views
                        0 likes
                        Last Post seqadmin  
                        Started by seqadmin, 03-27-2024, 06:07 PM
                        0 responses
                        13 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
                        70 views
                        0 likes
                        Last Post seqadmin  
                        Working...
                        X