Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Question about SAM file.Thanks.

    Hello guys

    I have a very basic question.

    I got a sam file after mapping by BWA and I found lots of format like this:


    ILLUMINA-XXXXXX:7:FC6XXXXXXXX:2:1:8471:2169 141 * 0 0 * * 0 0 TTTTTGTTCAAAAACACTCTGGAACTTAAAAGTAAAACTCTTCCACGTACATCTCTGGCTTATTGGTGTCTTTTTCTCTTTTTGAAGGCGTTTTGAAATGG IIIIIIIIIIIIIHIIIIIIIIIIIIIFIIIIIIIIIIHIGIIIGIIIIIIIDGIIIIIGIBHGIIEGFGGIIHIDDDIIIIHHB>HC<F?C>EECAFGGD


    Others like this

    ILLUMINA-XXXXXX:7:FCXXXXXXXX:2:1:13814:2169 163 chr24 42647385 60 101M = 42647444 160 AAACATTGTTTATCAACATTAGATGTAACATAAATCTCTAATGTACATACCTGATGGGAAAACAAGTAAAACAATTCATATTGATGTCAACCAAATGCATA GIDGGGECEGAAGGGG@GGGGGGGGDGBIIIIHDIIIHIHGGHIIEDHIIHIIIIHIIIIIIGHHIHIHHGHDIIGHHDHBEEDIIIG<D@DDDGGGGDDD XT:A:U NM:i:3 SM:i:23 AM:i:23 X0:i:1 X1:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:44G4A15C35 XA:Z:chr24,-42545737,101M,4;

    Is previous one a unmapping reads?

    Thanks a lot!
    Last edited by illuminaGA; 10-17-2013, 01:34 PM.

  • #2
    The first read isn't mapped (neither is its mate), the second is (and so is its mate). When trying to figure out a read's flag (the second column), it's convenient to have a calculator open in "programmer" mode, so you can just type a number and see visually which bits are set.

    Comment


    • #3
      [QUOTE=dpryan;119110]The first read isn't mapped (neither is its mate), the second is (and so is its mate). When trying to figure out a read's flag (the second column), it's convenient to have a calculator open in "programmer" mode, so you can just type a number and see visually which bits are set.[/QUOT

      Thank you so much!

      Comment


      • #4
        Originally posted by illuminaGA View Post
        Hello guys

        I have a very basic question.

        I got a sam file after mapping by BWA and I found lots of format like this:


        ILLUMINA-XXXXXX:7:FC6XXXXXXXX:2:1:8471:2169 141 * 0 0 * * 0 0 TTTTTGTTCAAAAACACTCTGGAACTTAAAAGTAAAACTCTTCCACGTACATCTCTGGCTTATTGGTGTCTTTTTCTCTTTTTGAAGGCGTTTTGAAATGG IIIIIIIIIIIIIHIIIIIIIIIIIIIFIIIIIIIIIIHIGIIIGIIIIIIIDGIIIIIGIBHGIIEGFGGIIHIDDDIIIIHHB>HC<F?C>EECAFGGD


        Others like this

        ILLUMINA-XXXXXX:7:FCXXXXXXXX:2:1:13814:2169 163 chr24 42647385 60 101M = 42647444 160 AAACATTGTTTATCAACATTAGATGTAACATAAATCTCTAATGTACATACCTGATGGGAAAACAAGTAAAACAATTCATATTGATGTCAACCAAATGCATA GIDGGGECEGAAGGGG@GGGGGGGGDGBIIIIHDIIIHIHGGHIIEDHIIHIIIIHIIIIIIGHHIHIHHGHDIIGHHDHBEEDIIIG<D@DDDGGGGDDD XT:A:U NM:i:3 SM:i:23 AM:i:23 X0:i:1 X1:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:44G4A15C35 XA:Z:chr24,-42545737,101M,4;

        Is previous one a unmapping reads?

        Thanks a lot!

        There is a tool from picard


        use the number at second column (e.g. for the first read: 141 )

        Comment


        • #5
          Originally posted by harryzs View Post
          There is a tool from picard


          use the number at second column (e.g. for the first read: 141 )
          Thank you so much!!

          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
          7 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          7 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
          66 views
          0 likes
          Last Post seqadmin  
          Working...
          X