Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • fpepin
    replied
    Ok.

    I thought about it afterward but then I started worrying about cross-posting.

    I'll move it there.

    Leave a comment:


  • flxlex
    replied
    You might have a bigger chance of getting an answer by reposting the question in, for example, the bioinformatics forum...

    Leave a comment:


  • fpepin
    started a topic Hi and a hopefully not to dumb question

    Hi and a hopefully not to dumb question

    Hi everyone,

    I've recently been "promoted" from the microarray analysis world now that the previous guy babysitting our dna sequencing projects has left for greener pastures.

    You all come very highly recommended, so I'm hoping you can help me go from asking lots of dumb questions to being able to contribute at least a bit.

    With the caveat that I'm not sure if this has been discussed ad nauseam and I whether I've got enough details to be clear, here's my little problem:

    We've got DNA sequencing for exome-capture run for about 40 cancer cell lines. I'm finding some very common differences from the reference genome that isn't in dbSNP or 1000 Genomes and I was wondering if anyone could help explain what it is and if there is a reasonable way to filter off these features.

    One example is A1BG with a T109G (ACC->CCC at position 325 [transcript ENST00000453054], reverse strand), chr19:58862835 T->G (hg19, chr19:63554647 for hg18). I have that mutation on 37/42 samples.

    The various QC metrics are good and the reads are nicely clustering around exonic regions as expected. I checked with a known gene (p53) and the resulting mutations also match up.

    The fact that it appears in so many samples and isn't in either dbSNP or 1000 genomes worries me a little bit. We have over 100 genes that have unknown mutations in over 30 samples, so I'd love to have a decent filter for them.
    Last edited by fpepin; 02-08-2011, 05:34 PM. Reason: typo

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM
  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 05-14-2024, 07:03 AM
0 responses
20 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-10-2024, 06:35 AM
0 responses
44 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
54 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
42 views
0 likes
Last Post seqadmin  
Working...
X