Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Trimmomatic palindrome clipping (MIN_PREFIX=8)

    I have Illumina RNA-Seq data with extremely short fragment sizes (150bp for 100bpPE reads). I am using Trimmomatic because I like how the palindrome clipping handles read-through (and bonus points for handling orphans for me). However, after running Trimmomatic I still see residual adapter contamination in the last 7bp or less of the 3' end of some of the reads.

    Looking at the source code, I see there is a parameter MIN_PREFIX=8 (in IlluminaClippingTrimmer.java). When I change it to MIN_PREFIX=1, I get the desired result. I think I understand the code, but I don't code in Java. Is there a reason that I am missing that makes it a bad idea to lower this value? My reasoning is that if the left and right reads overlap in such a way that indicates read-through, even if only 1 base of the adapter was sequenced, then we can safely trim the small bit of adapter and throw out the second read.

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
19 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-10-2024, 06:35 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
53 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