Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • what's the difference between a bam and a sorted bam

    I have both and don't know what to do with either (i.e. how to analyze). I was going to use NCBI genome workbench since it seemed to be the least convoluted and it works with windows.

  • #2
    Sorted BAM has the data sorted by chromosomes/contigs/scaffolds whatever is in your reference genome. In order to efficiently display/access the data the BAM file has to be sorted.

    For viewing aligned/sorted BAM files use integrated genome viewer (IGV) on windows. Unfortunately Broad's website appears to be down for maintenance till Monday but the URL you will want is: http://www.broadinstitute.org/igv/

    You can try IGB in the mean time: http://bioviz.org/igb/index.html
    Last edited by GenoMax; 10-17-2013, 02:17 PM.

    Comment


    • #3
      Originally posted by GenoMax View Post
      Sorted BAM has the data sorted by chromosomes/contigs/scaffolds whatever is in your reference genome. In order to efficiently display/access the data the BAM file has to be sorted.

      For viewing aligned/sorted BAM files use integrated genome viewer (IGV) on windows. Unfortunately Broad's website appears to be down for maintenance till Monday but the URL you will want is: http://www.broadinstitute.org/igv/

      You can try IGB in the mean time: http://bioviz.org/igb/index.html
      Thanks for the info. Unfortunately, it's IGB is not allowing me to install the program and keeps saying error:could not create a virtual java machine.

      Comment


      • #4
        Scratch that, I was able to download the low memory version, even though my computer was 4Gb of ram... I am able to open my .sam file in IGB but neither of my .bam (bam and sorted bam) will open. It says "Failed to authenticate server" when I try to open file.

        Comment


        • #5
          What genome are you working with?

          Have you indexed your sorted BAM?
          Code:
          $samtools index sorted.bam
          Here is another option to try: http://bioinf.scri.ac.uk/tablet/
          Last edited by GenoMax; 10-17-2013, 03:03 PM.

          Comment


          • #6
            Originally posted by GenoMax View Post
            What genome are you working with?

            Have you indexed your sorted BAM?
            Code:
            $samtools index sorted.bam
            Here is another option to try: http://bioinf.scri.ac.uk/tablet/
            I used Bowtie 2 to align against MM10 (mouse genome).

            I have not yet created an indexed BAM since the bowtie 2 manual didn't mention anything about that. But it looks like it's required, so I"ll do that tomorrow when I'm at my Linux computer.

            It looks like my SAM file is aligning to IGB mRNA but I don't know what the genes are since they're given cryptic names.

            Comment


            • #7
              Originally posted by KnowNothing2 View Post
              I used Bowtie 2 to align against MM10 (mouse genome).

              It looks like my SAM file is aligning to IGB mRNA but I don't know what the genes are since they're given cryptic names.
              You can download the mm10 GTF file here: ftp://ftp.ensembl.org/pub/current_gt...Cm38.73.gtf.gz IGB should be able to open that and give you gene annotations.

              Comment


              • #8
                Originally posted by GenoMax View Post
                You can download the mm10 GTF file here: ftp://ftp.ensembl.org/pub/current_gt...Cm38.73.gtf.gz IGB should be able to open that and give you gene annotations.
                Okay, I figured if I just downloaded an MM10 genome I'd be able to reference (right now I'm using Tablet). that said, I began downloading the mm10 genome from the Bowtie 2 website. Hopefully that does it.

                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
                8 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, Yesterday, 06:07 PM
                0 responses
                8 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