Header Leaderboard Ad

Collapse

newbler, parameters to improve my cDNA assembly de novo

Collapse

Announcement

Collapse
No announcement yet.
This topic is closed.
X
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • newbler, parameters to improve my cDNA assembly de novo

    I'm trying to assemble de novo cDNA reads from transcriptome of Begonia using Newbler but actually the result isn't really good... I've used the configured parameters since it's my first assembly. I would like to know, if there are someone who used to run Newbler, which parameters could I change in order to improve my results. That are the parameters:

    Input: minimum read length: 20 Computation: seed step:12 seed length:16 seed count:1 minimum overlap length:40 minimun overlap identity:90 alignment identity score: 2 alignment difference score:-3

    Thanks for all!

  • #2
    Closed due to double posting (bioinformatics forum)

    Comment

    Latest Articles

    Collapse

    • seqadmin
      A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
      by seqadmin


      ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

      01-24-2023, 01:19 PM
    • seqadmin
      Introduction to Single-Cell Sequencing
      by seqadmin
      Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

      The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
      ...
      01-09-2023, 03:10 PM

    ad_right_rmr

    Collapse
    Working...
    X