Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Vinn
    replied
    Thanks so much Brian for your advice. I will try as you suggested.

    Leave a comment:


  • Brian Bushnell
    replied
    Excessive trimming reduces accuracy, and will degrade the results of any experiment. If you want to be confident that bases are genomic rather than artificial, I suggest you follow this methodology:

    1) Map the reads to the reference (if you don't have a reference, you can make a quick assembly with Tadpole) with BBMap like this:

    Code:
    bbmap.sh in=reads.fq ref=ref.fa mhist=mhist.txt qhist=qhist.txt
    2) Plot mhist with R or Excel with a log-scale Y-axis to look at the positional error rates.

    If there is not an increased error rate in a region of the read, there is no reason to trim it. And conversely, it is prudent to trim if there is a high error rate at one end or the other.

    Leave a comment:


  • Vinn
    replied
    Thanks for your reply Brian. Just to be on a safe side, do you think it is better to trim the end off?

    Leave a comment:


  • Brian Bushnell
    replied
    Kmer-content spikiness at the beginning of the read is normal for many fragmentation methodologies and should not be removed. I'm not sure what's going on at the end, though...

    Leave a comment:


  • Vinn
    replied
    Thank you, I will read the thread through.

    Leave a comment:


  • GenoMax
    replied
    Take a look at @Brian's suggestions in this thread. I have provided a link for a specific post but take a look at the whole thread. He should be along with more later.

    Leave a comment:


  • Vinn
    replied
    Originally posted by GenoMax View Post
    What kind of analysis are you trying to do? In general I have never worried about k-mer warnings from FastQC.
    Hi GenoMax, thanks for your reply. I would like to do de novo assembly.

    Leave a comment:


  • GenoMax
    replied
    What kind of analysis are you trying to do? In general I have never worried about k-mer warnings from FastQC.

    Leave a comment:


  • Vinn
    started a topic K-mer content failed on 5' end - advice needed

    K-mer content failed on 5' end - advice needed

    Hi folks,

    I am trying to do adapter and low quality trimming of a fungal genome (prepared with Illumina DNA nano kit and sequenced with HiSeq 2000 100PE). After using BBduk to trim adapters and low quality reads as following

    >./bbduk.sh in1=R1.fastq.gz in2=R2.fastq.gz out1=R1_q25.fastq.gz out2=R2_q25.fastq.gz ktrim=r k=21 mink=11 hdist=2 tpe tbo ref=resources/adapters.fa qtrim=rl trimq=25

    Still FASTQC showed a K-mer content warning for both R1 and R2 reads [ https://goo.gl/photos/Lsyt7YJeQnjB8HQq5 ]. Can I have your opinion how shall I handle my data? Shall I just remove the first 20 bases to be on a safe side? Or it is normal behavior for a library prepared with the nano kit?

    Thanks in advance and have a great day!
    Last edited by Vinn; 04-21-2017, 06:47 AM.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X