Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • No coverage or very low coverage in the Complete Genomics data

    Hi,

    Has anyone worked on Complete Genomics data? Most of the exons in the data have no coverage or very low coverage (5-10 reads only) even though the reads are sequenced at 40X coverage. Can anyone explain why is it so?

    Thanks

    Regards

  • #2
    Hi! Is it really the exons only, that show reduced coverage and the rest of the genome shows 40x? Have you checked the mean of all exons or for one particular gene only? What kind of genome and data are you working with? In general I would say it's kind of normal to see differences in coverage over the genome, but I am not aware of a exon specific bias. However, if you look on a particular gene or even a gene-family, the coverage might be reduced because of homology regions and multimapped reads with low mapping quality that are filtered out. Maybe it is worth to have a look on the percentage of reads you are able to map against your reference. A high number of discarded sequences could be a hind of such an effect.

    Comment


    • #3
      I’m sorry, I didn’t explain the issue properly. I’m working on CG WGS data with avg read depth of 40x. The QC metrics looks good for all parameters and the alignment rate is 97.43%. However, I had used cgaTools to convert tsv files provided by CG to BAM. When I visualize these BAM files on IGV, I see minimal coverage at all exons and major parts of introns for all genes (See example image attached). The trend is normally scant coverage hills at junction of intron and exon. I believe something went wrong in my conversion step. Can anyone please suggest a solution for this?
      Or is there any other visualization tool specific for CG data that I should be using?”

      The IGV snapshots is attached herewith.

      Thanks in advance
      Attached Files
      Last edited by raman91; 01-09-2018, 01:48 AM.

      Comment


      • #4
        Hi! It could be an issue due to differing genome builds. Ich guess igv is using hg19 and reads are mapped to hg38.

        Comment


        • #5
          You should be able to Check this by zoom in to nucleotide Level in igv. If the reads Do Not Match the reference this would be a Hind. I am Not a 100% Sure but i believe igv only uses the coordinates and cigar of the bam and does Not care about matching nucleotides. So maybe it is just a slippage of coordinates between hg19 and 38.

          Comment


          • #6
            Thanks for your reply. I am pretty sure that the reads are mapped to hg19 build only. I checked the IGV browser too and the read sequence match to the reference sequence.

            Comment

            Latest Articles

            Collapse

            • 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
            • seqadmin
              Multiomics Techniques Advancing Disease Research
              by seqadmin


              New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

              A major leap in the field has
              ...
              02-08-2024, 06:33 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 02-28-2024, 06:12 AM
            0 responses
            27 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 02-23-2024, 04:11 PM
            0 responses
            74 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 02-21-2024, 08:52 AM
            0 responses
            81 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 02-20-2024, 08:57 AM
            0 responses
            69 views
            0 likes
            Last Post seqadmin  
            Working...
            X