Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Working with BAM files

    Hi everybody!

    This is my first thread in this forum.
    Recently, I started an internship in a bioinformatics research group. Unfortunately, I have only little experience regarding programming, bioinformatic data handling, ...
    I have basic programming skills in Bash, Python and R, but that's it.

    My task is to inspect three BAM files (> 1 Mio reads). The three BAM files were generated using different methods. I want to find out which BAM files contain the same reads, which reads are only in BAM file 1, which reads are missing in BAM file 3 and so on.

    Can you give me some advice how to deal with this task? Do you have experiences in BAM file handling?

    Many greetings!

  • #2
    more details

    Maybe I should add some information:
    We took one sample and generated the BAM files using three different pipelines.
    At the moment, we are only interested in the read names (first column of the BAM files) and want to find out which reads are present in all BAM files, which are present in file 1, file 2, file 3...

    Comment


    • #3
      You could simply get the names (field 1 as you already note, sort | uniq them in bash) and do a "comm" comparison of the three results. If your aim is just to find which reads are present in all three files.

      Comment


      • #4
        progress

        Thank you for the answer!

        I already extracted the read names from all files separately using:

        > samtools sort -n bam_filename | samtools view | awk -F "\t" '{print $1}' > output_filename

        Now, my supervisor supposed to use python to do the rest of the task...
        Or can you recommend another possibility?

        Greetings

        Comment


        • #5
          I looked the "comm" command up. Sounds promising, but I am not sure if this works for such big data files with > 1 Million reads. Do you have an idea for a smart python-based solution?

          Nevertheless, I will try it also using comm.

          Greetings

          Comment


          • #6
            If this is an assignment then use what you have to but comm should work (as long as you have enough RAM available). Since you are working with only read names (if you are not then you should).

            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
            11 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            51 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            68 views
            0 likes
            Last Post seqadmin  
            Working...
            X