Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie beginner question...

    I am trying to perform an alignment of a fastq file using bowtie.

    bowtie -q -p 8 -v 3 -a -m 600 --best --strata /inputfolder/inputFILE.fq

    I get the following error:
    No query or output file specified!

    I also tried the following:
    bowtie -q /inputfolder/inputFILE.fq -p 8 -v 3 -a -m 600 --best --strata

    and received the same message.

    I'm not sure what I am doing wrong but I feel like it's something very simple. Any help would be greatly appreciated.

  • #2
    Hi milesgr,

    Did you prepare the index files for Bowtie? You need to specify the base in the command.

    Douglas

    Comment


    • #3
      Thanks for the quick response...I originally forgot to include the index (so I fixed that), but I did have a build of it already. One more question...

      I built the script to run by (see the below script) changing folders to the folder containing the scripts, which is writable. I then (below this) call bowtie using the full path, referencing the index file (in index_folder) and the fastq file (in folder fastqpath). Neither index_folder or fastqpath are writable folders. My question is, to which folder will the output file be attempted? I assumed it was the working directory, but I wanted to make sure. Furthermore, if I wanted the output file to go to a different folder, how would I accomplish this? Thanks.

      cd script_directory

      /full_path/bowtie -q -p 8 -v 3 -a -m 600 --best --strata /index_folder /fastqpath/fastqfile.fq

      Comment


      • #4
        Your current command, as is, will print the output to the screen. Check the bowtie online manual on the "output" session; it has many options for its output. As to redirect the output to a different directory, just specify the path to it and make sure the directory is already there (and as you are already aware, writable).

        Douglas

        Comment


        • #5
          I read up on this and I guess my last (hopefully) question is:

          If I add the --sam as shown below, this should output to a sam format, correct? Further, when you specify, "As to redirect the output to a different directory, just specify the path to it and make sure the directory is already there.", what do you mean just specify the path to it? Where would I place that specification?

          /full_path/bowtie -q -p 8 -v 3 -a -m 600 --best --strata --sam /index_folder /fastqpath/fastqfile.fq

          Say, for instance I wanted to output the .sam file to /home/temp, could you do me a favor and put that in the command so I could see an example of this? Thanks again for all your help...I really appreciate it.

          Comment


          • #6
            /full_path/bowtie -q -p 8 -v 3 -a -m 600 --best --strata --sam /index_folder /fastqpath/fastqfile.fq > /home/temp/bowtie_out.sam

            Comment


            • #7
              batch bowtie alignment

              Firstly I must say I am a new to the linus and bowtie.

              My questions are
              1 I did demultilexing using CASAVA, and got a bunch of fatsq.gz files, then I did unzip of all the files. Should I do the alignment with bowtie file by file individually or write a loop or use a batch file to do the alignment?

              2 After I get the alignment, may I come back to use the CASAVA? or I had better to use the downstream softwares such as Myrna (paper) ,TopHat (paper), Cufflinks (paper),RNASEQR (paper).

              many thanks in advance.

              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
              10 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              9 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