Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • yvan.wenger
    replied
    Ooops, I*should have had a more careful look. While I*don't know what is exactly in the share/adapter.jf I*made my own:

    ../bin/jellyfish count -m 24 -s 5k -C -t 10 -o adapters_yvan.jf adapters.fa && mv adapter.jf adapter.jf_old && ln -s adapters_yvan.jf adapter.jf

    And it works well. I could have deleted the post but some might find it useful.

    Best,

    Yvan

    Leave a comment:


  • yvan.wenger
    started a topic MaSuRCA adapter trimming

    MaSuRCA adapter trimming

    Hello,

    I am currently trying MaSuRCA, I get nice results but I think they can be further improved.

    I made some test on a subset of reads, with or without clipping adapters before passing it to MaSuRCA. As advised in the short manual, I got better results with the full reads.

    When quorum starts it says in quorum.err: "Loading contaminant sequences", so I assume that there is somewhere a contaminant library, such as for example masurca/share/adapters.jf

    in the output PREFIX.cor.fa, I have plenty of my adapters, how can I specify my adapter sequences to quorum/MaSuRCA? Should I make a new adapters.jf file? My adapters are simple illumina TruSeq.

    Has somebody done that?

    Many thanks for all your thoughts !

    Yvan

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
24 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
58 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
45 views
0 likes
Last Post seqadmin  
Working...
X