Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • define if two RNA-seq samples from one individual

    hello,

    i have two RNA-seq libraries (~10 mio 50 PE) from tumor cells and i want to know if these are from the same person.

    which is the easiest way to do this. as control i have other RNA-seq libraries from other persons...

    thank you in advance,

    dietmar

  • #2
    You could compare their SNPs. The number of differences due to somatic mutations should be relatively small, and you could filter out any that aren't in dbSNP. You'll also want to filter out cases where a SNP is called in one sample but not in another because the gene expression is too low. A program like SomaticSniper that directly compares two bam files might be the best way to go.

    Comment


    • #3
      If you also had independent SNP chip data then it would be a good control to compare.

      Comment


      • #4
        @alec,

        SomaticSniper would be the perfect answer, but unfortunately i get no results for either a same-individual pair or a different-individual pair...

        the program seems to work - i get no errors - but the output-file is empty.

        perhaps this program works only with exom or genomic data, not with RNA-seq data?

        knows someone else a similar (easy usable) program especially for RNA-seq data. i don't want to implement a complete SNP analysis pipeline...

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Choosing Between NGS and qPCR
          by seqadmin



          Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
          10-18-2024, 07:11 AM
        • seqadmin
          Non-Coding RNA Research and Technologies
          by seqadmin




          Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.

          Nobel Prize for MicroRNA Discovery
          This week,...
          10-07-2024, 08:07 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:09 AM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-30-2024, 05:31 AM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-24-2024, 06:58 AM
        0 responses
        21 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-23-2024, 08:43 AM
        0 responses
        52 views
        0 likes
        Last Post seqadmin  
        Working...
        X