Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • NGS data analysis - help

    Hello everyone!

    I am a 1st year PhD Biochemistry student who is doing NGS for the first time (also the first time in our research group).

    Long-story short: We have two mutant libraries (484 and 1024 unique clones), both having two different barcodes and we are planning to pool them and sequence together. PCR amplicons will be 180 bp long, and they will only differ in 6 bp which is in the middle of the sequence.

    Sequencing will be done on Illumina platform, here are the specs:
    - Technology: Illumina NovaSeq
    - Run type: Paired end
    - Read length: 2 x 150 bp
    - Guaranteed 5 million read pairs (10 million reads) per package (+/- 3%)
    - Guaranteed 1.5 Gb raw data per package (+/- 3%)
    Deliverables: FastQ Files (sequences and quality scores)

    Since I am doing this for the first time, I have no experience in data analysis.
    I would like to do basic things: merging of overlapping reads, tag sorting and counting/calculating percentage of each variant. If anyone can recommend me software for data analysis, which is suitable for inexperienced user like me, to run on Windows preferably, but Linux would also work.

    If you have any other advice/recommendation it will be more than welcome!

    Thank you.

    Best regards

Latest Articles

Collapse

  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-14-2024, 06:13 AM
0 responses
34 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-08-2024, 08:03 AM
0 responses
72 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-07-2024, 08:13 AM
0 responses
82 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-06-2024, 09:51 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X