Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • question about tophat

    I am running tophat index/mm9 1.fastq

    to get accepted_hist.bam

    The running process has no error. But 1.fastq has 1Gb, accepted_hist.bam only has 470K.

    So What does it mean? It means only a few reads has mapped to reference genome?

    I downloaded mm9 from bowtie website and contructed a .fa file using bowtie-inspect mm9 > mm9.fa

    Anyone know this problem?

    thanks!

  • #2
    I am curious why no people reply this? anyone can help?

    Comment


    • #3
      Did you check look at your alignment file to see if anything was aligned or check the tophat log files?

      Comment


      • #4
        thanks, I have checked my result , I really got some result but the result number is so small.

        Comment


        • #5
          Originally posted by chadn737 View Post
          Did you check look at your alignment file to see if anything was aligned or check the tophat log files?
          Hi chadn737,

          May you recommend some good method to extract gene expression from RNA seq data.

          Now I am using tophat and cufflinks but the result seems not I want.

          BTW, does the reference genome mm9 I used is right?

          Comment


          • #6
            Originally posted by camelbbs View Post
            I am running tophat index/mm9 1.fastq

            to get accepted_hist.bam

            The running process has no error. But 1.fastq has 1Gb, accepted_hist.bam only has 470K.

            So What does it mean? It means only a few reads has mapped to reference genome?

            I downloaded mm9 from bowtie website and contructed a .fa file using bowtie-inspect mm9 > mm9.fa

            Anyone know this problem?

            thanks!
            This is absolutely normal. accepted_hits.bam is in the binary BAM format which uses much less space than fastq (which is in text format).

            Comment


            • #7
              Originally posted by shurjo
              This is absolutely normal. accepted_hits.bam is in the binary BAM format which uses much less space than fastq (which is in text format).
              True, but 470K is a very small bam file, even for a small data set of only 1GB.

              Comment


              • #8
                Originally posted by chadn737 View Post
                True, but 470K is a very small bam file, even for a small data set of only 1GB.
                Agreed. Maybe we will get a better insight after camelbbs looks at the actual BAM file to see what's in it.

                Another option would be to run FastQC on the input file to check the quality of the reads.

                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