Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cufflinks won't read my GTF file

    Hi all,

    I am trying to run cufflinks and cuffdiff with an annotation file (GTF)
    I've been trying to use a file that I downloaded from the ucsc by creating a table with the needed information and sending it to galaxy.
    Now I would like to use it on my pc (not on galaxy) and I keep on getting this error :
    "Error: cannot open reference GTF file miranno.gtf for reading"

    The annotation file has full permissions to all users ...

    and it looks like this:

    chr1 hg18_wgRna exon 1092347 1092441 960.000000 + . gene_id "hsa-mir-200b"; transcript_id "hsa-mir-200b";
    chr1 hg18_wgRna exon 1093106 1093195 960.000000 + . gene_id "hsa-mir-200a"; transcript_id "hsa-mir-200a";
    chr1 hg18_wgRna exon 1094248 1094330 960.000000 + . gene_id "hsa-mir-429"; transcript_id "hsa-mir-429";
    chr1 hg18_wgRna exon 3467119 3467214 480.000000 - . gene_id "hsa-mir-551a"; transcript_id "hsa-mir-551a";
    chr1 hg18_wgRna exon 9134314 9134423 480.000000 - . gene_id "hsa-mir-34a"; transcript_id "hsa-mir-34a";
    chr1 hg18_wgRna exon 19096152 19096229 480.000000 - . gene_id "hsa-mir-1290"; transcript_id "hsa-mir-1290";
    chr1 hg18_wgRna exon 21187394 21187512 480.000000 - . gene_id "hsa-mir-1256"; transcript_id "hsa-mir-1256";
    chr1 hg18_wgRna exon 26753620 26753671 960.000000 + . gene_id "hsa-mir-1976"; transcript_id "hsa-mir-1976";

    What might be the problem?

    Thanks in advance !

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 08:47 AM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Working...
X