Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • swbarnes2
    replied
    It's not an inconsistancy, exactly. Your problem is not that a bunch of reads are inaccurate. It's probably what the template really looks like; a mix of two different DNAs. It's almost certainly because the sample that was given to you was a mix of two slightly different populations. It happens, you should tell your submitters what you are seeing. You could confirm some with sanger sequencing, to be sure.

    Hopefully, your mutant samples should be clonal, and not have mixed letters. What you'll want to do is check everything that looks like a possible SNP in your mutant, and see if the wt shows a trace of the mutant letter. If it does, than your mutant has the alternate letter because of descent, not becuase of mutation. The mutations you are most interested in are those where the wt doesn't show a trace of the alternate letter seen in the mutant.

    Leave a comment:


  • biocc
    replied
    thanks

    Originally posted by swbarnes2 View Post
    I do bacteria, and I see mixed samples all the time, too.

    The simplest explanation I can think of is that you've got a non-clonal population.

    For instance, I've seen cases where I was given a non-clonal parental strain, and some offspring resistant strains, and there will be some mutations that are clean in the offspring, but mixed in the parental. I've tested some such loci with sanger sequencing, and they pretty much always confirm the Illumina data.
    thanks for your reply. this question puzzled me for a long time. since I focus on the difference between mutated strain and WT, it may be difficulty to determine the SNPs from the mixed samples which you inferred. to verify the SNPs which BWA and samtoos gave, i visualized the alignment by Tablet, and found some reads support the SNP, some do not in almost of all SNPs. how to deal with this inconsistent? could you give me some advice ?

    Leave a comment:


  • swbarnes2
    replied
    I do bacteria, and I see mixed samples all the time, too.

    The simplest explanation I can think of is that you've got a non-clonal population.

    For instance, I've seen cases where I was given a non-clonal parental strain, and some offspring resistant strains, and there will be some mutations that are clean in the offspring, but mixed in the parental. I've tested some such loci with sanger sequencing, and they pretty much always confirm the Illumina data.

    Leave a comment:


  • biocc
    started a topic Heterozygote and homozygote

    Heterozygote and homozygote

    hi, when I resequenced a bacteria and aligned with reference , i found heterozygote is very common. since my sample is lab strain and bacteria is haploid, i do not understand this phenomenon. could someone explain for me? thanks

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 06-21-2024, 07:49 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-20-2024, 07:23 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-17-2024, 06:54 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
25 views
0 likes
Last Post seqadmin  
Working...
X