Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie and Tophat in disagreement with alignment

    Hi all,

    I had a question about running bowtie and tophat. If I run bowtie (flags: -p 4 -S --un -v 3; paired-end) independently of tophat, I get very different results when looking at what % of the reads were mapped to my reference genome (hg18). Bowtie by itself aligns 38,474,274 of 87,783,858 reads to hg18, whereas when tophat is run (flags: -p 4 -r 20; paired-end) it maps 69,190,587 reads. Does anyone have an idea why they would differ so greatly?

    The data is 76bp paired end from cancer patients done on the GAIIx.

  • #2
    Tophat will map more reads than Bowtie because Tophat detects the splicing junction first which will make the reads spanning junctions mappable.
    Originally posted by NM_010117 View Post
    Hi all,

    I had a question about running bowtie and tophat. If I run bowtie (flags: -p 4 -S --un -v 3; paired-end) independently of tophat, I get very different results when looking at what % of the reads were mapped to my reference genome (hg18). Bowtie by itself aligns 38,474,274 of 87,783,858 reads to hg18, whereas when tophat is run (flags: -p 4 -r 20; paired-end) it maps 69,190,587 reads. Does anyone have an idea why they would differ so greatly?

    The data is 76bp paired end from cancer patients done on the GAIIx.

    Comment


    • #3
      That makes sense, but surely it shouldn't have such a large impact that it doubles the number of reads aligned to the genome?

      Comment


      • #4
        Originally posted by NM_010117 View Post
        That makes sense, but surely it shouldn't have such a large impact that it doubles the number of reads aligned to the genome?
        You observations sound perfectly in agreement with what I would expect. The average size of a exon in the human genome is 200bp. Your reads are 76nt. If the leftmost mapping position of a read is < 76bp from the end of the exon it will fail to map using bowtie. This 76bp "dead window" if you will represents 38% of the average exon length. You observed a reduction of 44%; you're in the ballbark.

        Comment


        • #5
          Originally posted by kmcarr View Post
          You observations sound perfectly in agreement with what I would expect. The average size of a exon in the human genome is 200bp. Your reads are 76nt. If the leftmost mapping position of a read is < 76bp from the end of the exon it will fail to map using bowtie. This 76bp "dead window" if you will represents 38% of the average exon length. You observed a reduction of 44%; you're in the ballbark.
          Ah ha! Ok, that makes perfect sense. So tophat and bowtie are more or less in agreement with eachother; I'm just interpreting the results incorrectly. Well, at least it's promising to know that the mapping was done correctly at least.

          Thanks for the help.

          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