Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mlafave
    replied
    Thanks for your help, everyone!

    Leave a comment:


  • adamyao
    replied
    You can try VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do). It should be able to provide what you want with graphical output in real time. By using "Query by Bacth" can give you results for multiple positions. If you have thousands of positions to query then you can use MegaQuery.

    VarioWatch only supports human genome.

    Leave a comment:


  • ishmael
    replied

    I would suggest diffReps. There is a script named region_analysis.pl.
    It could read bed format files and generate annotated files fitting most your demands.
    The output looks like:
    Chrom Start End GName TName Strand TSS TES Feature D2TSS
    chr1 2986341 2986690 Ust NM_001108458 - 2868195 3158231 Genebody 171715.5

    Refseq and ensembl annotation surpported, but only human, mouse, rat genomes available now.

    Leave a comment:


  • adaptivegenome
    replied
    snpEff is good to, very simple to use

    Leave a comment:


  • colindaven
    replied
    Try Bedtools.

    You'll need an annotation of course.

    Galaxy is also good - see the interval functions there.

    Leave a comment:


  • mlafave
    started a topic Genome annotation program/script?

    Genome annotation program/script?

    Hi, all - I'm looking for a way to annotate a list of positions in a genome. Basically, I have a list of positions that looks like this:

    chr1 3026294
    chr1 30175158
    chr2 17717521

    ...and so on. I want to know:
    1) the names of the gene(s) (if any) that overlap that position
    2) the orientation of those genes, and
    3) which part of the gene the listed position is (5' UTR, second exon, fourth intron, etc.).

    I feel like someone must have made something to do this before, but I don't know where to look. Any ideas? Thanks!

Latest Articles

Collapse

  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 05-24-2024, 07:15 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 10:28 AM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 07:35 AM
0 responses
20 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Working...
X