Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Overlapping Paired End reads - questions...

    Hi guys,

    I've just received my first RNA-Seq data back from sequencing.

    The company I used did chemical RNA fragmentation, which apparently produces more size-consistent, albeit smaller, fragments and thus, with 100bp PE reads, I have overlap in the majority of reads.

    From reading these discussions it seem like I have two options: either merge into long SE reads, or run in top hat with -ve insert length specified. I think I'm going to try both for comparison, but I have a few questions:

    Firstly, what is the best tool for assembling overlapping reads? I have seen mention of -

    Stitch (http://github.com/audy/stitch),
    SHERA (http://almlab.mit.edu/vibrioGenomes/SHERA_temp/),
    SeqPrep (http://seqanswers.com/wiki/SeqPrep) and
    FLASH (http://genomics.jhu.edu/software/FLASH/index.shtml)

    What are the recommendations?

    Secondly, If I'm to specify the negative insert length in tophat, I need to know the extent which they overlap - do any/all of the these programmes do this?

    Many thanks,

    Nick

Latest Articles

Collapse

  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM
  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:12 AM
0 responses
19 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-23-2024, 04:11 PM
0 responses
67 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
75 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
66 views
0 likes
Last Post seqadmin  
Working...
X