Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Hisat2 vs. bowtie2 - why does bowtie2 mapped better?

    Hi all,

    I have 358 pairs pair-end samples from human genome. I am looking for the best way to map them to the reference for differential expression analysis.
    I have tested the STAR aligner as well as tophat and Hisat2, but somehow they all fail to map.

    Than I have tested the bowtie2 algorithm and found out, that it maps a lot better (AFAIK) than all the others.
    As the mapping with bowtie2 takes longer than Hisat2 and or STAR, I would like to try and understand first if the results are correct.
    I thought, Hisat2 and STAR work not only faster, but suppose to also better.

    These are the commands I am using to map my files

    Code:
    hisat2 -p 15 -x /home/yeroslaviz/genomes/Mus_musculus/HISAT2/grcm38/genome -1 700APAAXX_1_1.fastq.gz -2 700APAAXX_1_2.fastq.gz -S 700APAAXX_1_2.hisat2.sam
    
    bowtie2 --very-sensitive -p 15 --un tmp.unmapped -x /home/yeroslaviz/genomes/Homo_sapiens/GRCh38.p3/bowtie2indexed/Hsapiens.GRCh38 -1 700APAAXX_1_1.fastq.gz -2 700APAAXX_1_2.fastq.gz -S 700APAAXX_1_2.sam
    and the results i am getting from the mapping:

    Code:
    [B]hisat2[/B]
    
    33778368 reads; of these:
      33778368 (100.00%) were paired; of these:
        32551450 (96.37%) aligned concordantly 0 times
        564637 (1.67%) aligned concordantly exactly 1 time
        662281 (1.96%) aligned concordantly >1 times
        ----
        32551450 pairs aligned concordantly 0 times; of these:
          20823 (0.06%) aligned discordantly 1 time
        ----
        32530627 pairs aligned 0 times concordantly or discordantly; of these:
          65061254 mates make up the pairs; of these:
            62207013 (95.61%) aligned 0 times
            1237583 (1.90%) aligned exactly 1 time
            1616658 (2.48%) aligned >1 times
    7.92% overall alignment rate
    
    [B]bowtie2[/B]
    
    
    33778368 reads; of these:
      33778368 (100.00%) were paired; of these:
        11345742 (33.59%) aligned concordantly 0 times
        16268991 (48.16%) aligned concordantly exactly 1 time
        6163635 (18.25%) aligned concordantly >1 times
        ----
        11345742 pairs aligned concordantly 0 times; of these:
          2699536 (23.79%) aligned discordantly 1 time
        ----
        8646206 pairs aligned 0 times concordantly or discordantly; of these:
          17292412 mates make up the pairs; of these:
            12165533 (70.35%) aligned 0 times
            3229431 (18.68%) aligned exactly 1 time
            1897448 (10.97%) aligned >1 times
    81.99% overall alignment rate
    Can someone explain to me, why bowtie2 performs better here?


    thanks

  • #2
    You're aligning to human with bowtie2 and mouse with hisat2...

    Comment


    • #3
      yes I have seen that. I am trying to delete the post until I can recheck the results, but it was too late

      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