Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Transfer a whole genome with .bam format

    Dear all,

    Do you have experience to transfer a whole genome of short-reads with ~35X sequenced by Illumina GA to .bam format using samtools? I feel very strange when I got more than 500G data. I addition, how can you extract chromosomes one by one and sort as well as index them? Thank you very much!

    Wuhoucdc

  • #2
    Originally posted by wuhoucdc View Post
    Dear all,

    Do you have experience to transfer a whole genome of short-reads with ~35X sequenced by Illumina GA to .bam format using samtools? I feel very strange when I got more than 500G data. I addition, how can you extract chromosomes one by one and sort as well as index them? Thank you very much!

    Wuhoucdc
    Never had a whole genome with that coverage :-( Sorted BAM may be slightly smaller.
    To extract a single chrom (or a single region) index it

    Code:
    samtools index file.bam
    and then extract your region

    Code:
    samtools view file.bam chrom[:start-end]
    HTH

    d

    Comment


    • #3
      Thanks for your answer, dawe.

      But why did you say "Never had a whole genome with that coverage "? Most of the sequenced individuals such as YH (PMID:18987735) and AK1 (PMID:19587683) were higher than that coverage (>35X).

      Wuhoucdc
      Last edited by wuhoucdc; 08-22-2010, 01:03 PM.

      Comment


      • #4
        Originally posted by wuhoucdc View Post
        Thanks for your answer, dawe.

        But why did you say "Never had a whole genome with that coverage "? Most of the sequenced individuals such as YH (PMID:18987735) and AK1 (PMID:19587683) were higher than that coverage (>35X).

        Wuhoucdc
        :-) I usually deal with ChIP-seq or exome analysis, never had a "first hand" high coverage of human genome.
        d

        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
        51 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