Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • Rookie
    Junior Member
    • Jun 2017
    • 1
    #1

    Pre-processing/QC of sequencing data Q's

    Hi all,

    Let me start of by saying, I have very very limited knowledge with regards to NGS and I'm truly the definition of a beginner. I have a couple of questions regarding certain steps during pre-processing of sequencing data from ANY platform, sorry if this has been asked before.

    1) Given a fastq file (from any platform), how does one identify the location and orientation of an adaptor sequence?

    2) How does one define the minimum bp length to infer adaptor? Or otherwise, if I'm working with a given fastq file, and I grep the adaptor sequence, obviously the full adaptor sequence doesn't appear in all the reads, so how low can I go with the amount of bp in the adaptor sequence I grep for?

    Hopefully these questions make sense.
    Tags: None
  • dpryan
    Devon Ryan
    • Jul 2011
    • 3478
    #2
    I've answered your identical post on biostars.

    Comment

    Previous template Next

    Latest Articles

    Collapse
    • SEQadmin2
      Cancer Drug Resistance: The Lingering Barrier to Rising Survival
      by SEQadmin2



      Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

      There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
      Today, 05:17 AM
    • GATTACAT
      Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by GATTACAT
      Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
      07-01-2026, 11:43 AM
    • SEQadmin2
      Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by SEQadmin2


      I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

      Here are nine questions we think about, in roughly the order they matter, before...
      06-18-2026, 07:11 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2
    Started by SEQadmin2, Today, 10:08 AM
    0 responses
    5 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    Today, 10:08 AM  
    Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2
    Started by SEQadmin2, Yesterday, 11:05 AM
    0 responses
    7 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    Yesterday, 11:05 AM  
    High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2
    Started by SEQadmin2, 07-02-2026, 11:08 AM
    0 responses
    29 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    07-02-2026, 11:08 AM  
    New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2
    Started by SEQadmin2, 06-30-2026, 05:37 AM
    0 responses
    28 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-30-2026, 05:37 AM  
    View All
    Working...