Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Custom reference when aligning male/ female NGS data to hg19 reference

    Hello everybody. I just wanted to ask if somebody has any experience in aligning sex specific data to hg19 genome build. I recently came accross a weird problem (which when you look at it indepth makes more sense) wherein I aligned my transcriptome sequencing data from primary breast cancer tumours to hg19, and a lot of the reads (approx 15000) were actually aligning to the y chromosome. I am using tophat 2.0 and bowtie 2.0 for the alignment.

    Has anybody faced this issue previously? Does it make sense to create a custom sex specific reference by removing the Y chromosome if your sequencing sample is female? I know 15000 is too small a percentage of reads when compared with the entire transcriptome having millions of reads, all the same this is an interesting question. Or is it that it really dosent matter a lot, and I am making a mountain out of a molehole? ANy thoughts would be mightily appreciated! thanks

  • #2
    Within the ENCODE consortium we use male/female references to avoid the false positives you saw (reads mapping to uniquely chrY in a female sample), as well as to avoid multi-mappers that map to both chrX and chrY in a female sample. Moreover, the autosomal (PAR) regions on chrY in the male genome are masked out.

    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