Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Problems importing GFFv3 Annotation into SeqMonk

    I am using SeqMonk version 1.0 and trying to add annotation files in GFFv3 format available at ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/

    Name Size Date Modified [parent directory]
    ref_Sscrofa10.2_scaffolds.gff3.gz 13.3 MB 3/7/12 9:26:00 PM
    ref_Sscrofa10.2_top_level.gff3.gz 13.0 MB 3/7/12 9:26:00 PM

    When I import them into SeqMonk, receive the following error after selecting FILE --> IMPORT ANNOTATION --> GFF/GTF:

    -----
    Request Generated Warnings...

    There were 530303 warnings when processing your request - showing the first 5000

    Couldn't find a chromosome called NC_010443.4
    Couldn't find a chromosome called NC_010443.4
    Couldn't find a chromosome called NC_010443.4
    Couldn't find a chromosome called NC_010443.4
    Couldn't find a chromosome called NC_010443.4
    Couldn't find a chromosome called NC_010443.4
    Couldn't find a chromosome called NC_010443.4
    ...

    ------

    It seems that the first column should be a chromosome designation (e.g. Chr1), but the GFFv3 format does not have this information in column 1.

    The SeqMonk changelog states that "Feature import from GFFv3 and GTF files" is supported, so I am not sure what my mistake is.

    Can anyone please help me with this?
    Thank you,
    jjw14

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
26 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
29 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
25 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
52 views
0 likes
Last Post seqadmin  
Working...
X