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  • Transcripome data analysis using CD-HITS

    We have sequenced a transcriptome of a species who does not have a sequenced genome, using 454 and our initial goal is to find a set of ESTs that represent genes. The 454 reads were assembled using Newbler 2.5 and the initial assembly gave ~26000 isotigs and 18,000. Contigs. After talking to the several people, I used CD-Hits program to combine the isotigs, contigs and singltons that were not assembled. After combining these sequences, I got ~4000 isotigs, ~17,000 contigs and ~30, 000 Singlton that were not assembled. Is this the correct way to do this? I couldn’t find any publication that has mentioned this method.

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  • 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

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