Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • changing bam files with mixed sample data to per sample

    I have five Bam files which has data of two to three samples togather as the samples were run in same channel. Is there any easiest way of seprating Bam file for each samples i.e can I split Bam files and combine per samples.
    Thanks.

  • #2
    I have just started this kind o analysis and as far as I could figure out people have suggested aligning all of your samples separately and denoting each with a unique group header, then merging your alignments.

    Comment


    • #3
      Bam per sample

      JackieBadger, Thanks.
      The problem which I have is each bam file is having two to three samples in it. So that means alignments are alreday performed? Any suggestion please how I can get it around to get bam per sample?

      Comment


      • #4
        Hi,
        You should be able to use samtools to split your bam file into multiple bam files.
        Here is how:

        # get the list of all sample names in INPUT.bam
        > samtools view -H INPUT.bam | awk '$0 ~ /^@RG/' | cut -f 2 | sed 's/ID://' > sample.list
        # for each sample 's' in sample.list; extract reads belong to this sample and save it as a bam file
        >for s in `cat sample.list ` ; do echo $s > sample.txt ; samtools view -bo ${s}.bam -hR sample.txt INPUT.bam ; done

        Hope this helps,

        Q

        Comment


        • #5
          Bam per sample

          Thanks qtrinh,

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Essential Discoveries and Tools in Epitranscriptomics
            by seqadmin




            The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
            Yesterday, 07:01 AM
          • seqadmin
            Current Approaches to Protein Sequencing
            by seqadmin


            Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
            04-04-2024, 04:25 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 04-11-2024, 12:08 PM
          0 responses
          58 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          53 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          45 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          55 views
          0 likes
          Last Post seqadmin  
          Working...
          X