Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • samstat versus tophat overall alignment rate %

    Hi group

    I am trying to map RNAseq single straneded paired end reads using tophat, the alignment rate I get using samtools falgstat is very good (~90%) however checking the logs files of tophat, specifically, bowties.left.keep.reads shows a very low overall alignment rate (~36%). Can someone please help me understand these parameters ?

    Thanks a lot
    Alyaa

    This is the tophat command I use:
    Code:
    $ tophat -g 1 -p 8 -G test.gtf -o test_thout --library-type fr-firststrand test R1_001.fastq R2_001.fastq
    This is the samtools flagstast command:
    Code:
     $ samtools flagstat accepted_hits.bam 
    36919320 + 0 in total (QC-passed reads + QC-failed reads)
    0 + 0 duplicates
    36919320 + 0 mapped (100.00%:-nan%)
    36919320 + 0 paired in sequencing
    18510302 + 0 read1
    18409018 + 0 read2
    33270470 + 0 properly paired (90.12%:-nan%)
    35338762 + 0 with itself and mate mapped
    1580558 + 0 singletons (4.28%:-nan%)
    406722 + 0 with mate mapped to a different chr
    87168 + 0 with mate mapped to a different chr (mapQ>=5)
    The logs files; bowtie.left_kept_reads.log
    Code:
    19786770 reads; of these:
      19786770 (100.00%) were unpaired; of these:
        12585633 (63.61%) aligned 0 times
        6908036 (34.91%) aligned exactly 1 time
        293101 (1.48%) aligned >1 times
    36.39% overall alignment rate

  • #2
    The accepted.bam file only contains mapped reads, not all of them, so the metrics will never be the same.

    Comment

    Latest Articles

    Collapse

    • 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
    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
      02-26-2024, 02:07 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-14-2024, 06:13 AM
    0 responses
    34 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-08-2024, 08:03 AM
    0 responses
    72 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-07-2024, 08:13 AM
    0 responses
    81 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-06-2024, 09:51 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X