Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cutPrimers: new tool for removing primer sequences from targeted NGS reads

    I present you new tool for removing primer sequences from NGS reads that were obtained during sequencing amplicon-based targeted panel. You can download it from https://github.com/aakechin/cutPrimers. It runs under any OS: Linux, Mac OS, Windows. If you have any question, you can ask me.

    Now, cutPrimers remove primer sequences only from unmapped reads in FASTQ-files. Later, it will be able to cut primer sequences also from mapped reads.

    I will be glad to answer for any questions about its use.

  • #2
    Thanks for updating. Does this work on every windows version?

    Comment


    • #3
      I tried it only on the Windows 7. Thank you for the question. I'll try it on the Windows XP and Windows 10

      Comment


      • #4
        Thanks for replying. Please let me know once you get some results of trying it on other OS. I had to discuss this with my Boss.

        Comment


        • #5
          I fixed some bugs for using in Windows. And I approved that it works now in Windows 7 and Windows 10. Windows XP will be a little bit later

          Comment


          • #6
            Unfortunately, cutPrimers does not work in Windows XP, because in Windows XP you can not install Python 3.6 and can not install Biopython module, because you can not install Visual Studio C++

            Comment


            • #7
              When are you going to add a BAM processing option?

              Comment


              • #8
                This can be done quickly and easily (I think during a week), but now I don't know how to efficiently read BAM-files in such a way that it will work in Windows. All exisiting Python modules need samtools that doesn't work in Windows. Maybe you know some variants or you can offer me some good algorithm?

                Comment


                • #9
                  Thanks for the prompt reply.
                  Maybe you could add this option at least for Linux users?

                  Comment


                  • #10
                    Originally posted by garrulus glandarius View Post
                    Thanks for the prompt reply.
                    Maybe you could add this option at least for Linux users?
                    I'm not sure that I will be able to do it in this year (2017). Maybe in 2018. Why don't you want to use cutPrimers before mapping?

                    Comment


                    • #11
                      Because, as far as I know, primer sequences aid in alignment process. Thanks for your answer.

                      Comment


                      • #12
                        Originally posted by garrulus glandarius View Post
                        Because, as far as I know, primer sequences aid in alignment process. Thanks for your answer.
                        It depends on the fragments that you study and the length of reads. In the most of cases, IMHO, sequence of amplicon without primers should be enough for good mapping.

                        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, Yesterday, 06:37 PM
                        0 responses
                        8 views
                        0 likes
                        Last Post seqadmin  
                        Started by seqadmin, Yesterday, 06:07 PM
                        0 responses
                        8 views
                        0 likes
                        Last Post seqadmin  
                        Started by seqadmin, 03-22-2024, 10:03 AM
                        0 responses
                        49 views
                        0 likes
                        Last Post seqadmin  
                        Started by seqadmin, 03-21-2024, 07:32 AM
                        0 responses
                        67 views
                        0 likes
                        Last Post seqadmin  
                        Working...
                        X