Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mgogol
    replied
    At UCSC, you can upload a custom track bed file, then use the table browser and do an intersection. You could also do this with galaxy "Fetch Sequences".

    On the command line, you have a number of options... bedtools getfasta comes to mind.

    Leave a comment:


  • dpryan
    replied
    If you have a bunch of ranges, then it might be most straight forward to just download the genomes in fasta format and just write a quick parser (samtools provides an fai_fetch function in the C API that can be given a genomic range and will return the sequence).

    Leave a comment:


  • ashkot
    started a topic Query Ensemble or USCS

    Query Ensemble or USCS

    Is there any automated way to get DNA sequences from UCSC genome browser or Ensemble for a list of chromosomal coordinates of interest.

    I have several chromosomal coordinates sets and cannot do it manually.

    Thanks in advance.

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 07:20 AM
0 responses
18 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
36 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
39 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
41 views
0 likes
Last Post seqadmin  
Working...
X