Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • "not_aligment" from the output of HTseq-count

    What's the meaning of "not_alignment" from the output of HTseq-count? The manual says it is the "reads in the Sam/Bam file without alignment". Does this mean the reads that are not mapped to the reference? or anything else? Thanks!

  • #2
    Yeah, these are just reads that didn't align. Whether the count for this is 0 or not will depend on the aligner that you're using (some don't put unaligned reads in the output SAM/BAM file, others do).

    Comment


    • #3
      Assuming that the file I used for input of HTseq-count includes the unaligned reads in the output BAM file, But the number of "no_alignment" reads doesn't match the number of reads not mapped to the reference. Any idea about this? Thanks!

      Comment


      • #4
        it should match. Maybe it's paired-end? (htseq-count counts read pairs, not reads)

        Comment


        • #5
          @flyingoyster: Try using the -o option to see what's going on in your case.

          Comment


          • #6
            @Simon Anders, Yes, My data is paired-end. If HTseq-count counts read pairs, not reads, that makes sense. Thanks a lot!
            @dpryan, I used Galaxy server, so not be able to choose options.

            If I want to calculate the number of reads within genes, is it right to substract the number of no_feature reads from the total number of mapped reads? Thanks!

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Exploring the Dynamics of the Tumor Microenvironment
              by seqadmin




              The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
              07-08-2024, 03:19 PM
            • seqadmin
              Exploring Human Diversity Through Large-Scale Omics
              by seqadmin


              In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
              06-25-2024, 06:43 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 07-19-2024, 07:20 AM
            0 responses
            29 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-16-2024, 05:49 AM
            0 responses
            42 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-15-2024, 06:53 AM
            0 responses
            50 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-10-2024, 07:30 AM
            0 responses
            43 views
            0 likes
            Last Post seqadmin  
            Working...
            X