Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie2 for creating output(fastq) that are not aligned with reference

    Hi there,
    I tried to get the output from bowtie2 those reads which did not align. As Bowtie2 has the option on paired reads to spit out fastq files of things that fail to align concordantly (--un-conc <path>), and it has the option to spit out fastq files of things than align concordantly (--al-conc <path>).
    I tried the following way:
    Anyone can give me some idea???

    Command: /home/zillur/Desktop/zillur/Tools/bowtie2-2.2.5/bowtie2-align-s --wrapper basic-0 -gbar 3 -x /home/zillur/Desktop/zillur/phd/Apecomplexan/B_microti/Reference/B_microti --passthrough -1 GI_7th_1.fastq -2 GI_7th_2.fastq
    (ERR): bowtie2-align exited with value 1
    [zillur@workstation01 Strain_GI]$ bowtie2 -x -gbar 3 /home/zillur/Desktop/zillur/phd/Apecomplexan/B_microti/Reference/B_microti -1 GI_7th_1.fastq -2 GI_7th_2.fastq --un-conc --al-conc
    perl: warning: Setting locale failed.
    perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
    perl: warning: Falling back to the standard locale ("C").
    Warning: Output file '3' was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
    Extra parameter(s) specified: "/home/zillur/Desktop/zillur/phd/Apecomplexan/B_microti/Reference/B_microti"
    Note that if <mates> files are specified using -1/-2, a <singles> file cannot
    also be specified. Please run bowtie separately for mates and singles.
    Error: Encountered internal Bowtie 2 exception (#1)
    Command: /home/zillur/Desktop/zillur/Tools/bowtie2-2.2.5/bowtie2-align-s --wrapper basic-0 -x -gbar --passthrough -1 GI_7th_1.fastq -2 GI_7th_2.fastq 3 /home/zillur/Desktop/zillur/phd/Apecomplexan/B_microti/Reference/B_microti
    (ERR): bowtie2-align exited with value 1

  • #2
    Hi,

    I do not know so well bowtie2 but same kind of options exist for bowtie, and you have to give an output file for unmapped guys...

    Comment


    • #3
      But how? Would you please to give me an example line.

      Comment


      • #4
        Code:
        --un-conc <output_file_un_conc> --al-conc <output_file_al_conc>
        Reading the manual tells you that bowtie2 will automatically add .1 and .2 to each output_file to distinguish the mates...

        Comment


        • #5
          Thank you very much for your kind reply. its working now.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            The Impact of AI in Genomic Medicine
            by seqadmin



            Article Coming Soon......
            Today, 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, 02-23-2024, 04:11 PM
          0 responses
          31 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-21-2024, 08:52 AM
          0 responses
          46 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-20-2024, 08:57 AM
          0 responses
          37 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-14-2024, 09:19 AM
          0 responses
          63 views
          0 likes
          Last Post seqadmin  
          Working...
          X