Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • stringtie error: GFF not recognized

    Hello,
    I'm trying to run stringtie with a reference genome, and I'm getting the following error:

    WARNING: no reference transcripts were found for the genomic sequences where reads were mapped!
    Please make sure the -G annotation file uses the same naming convention for the genome sequences.

    Similar posts indicate that there is some inconsistency between the reference genome fasta file that was used in the hisat2 step and the gff3 or gtf file that is used for stringtie. I can't see any inconsistency in my case. I'm stumped. I really, really hope someone can help!

    The reference genome fasta headers look like this:
    Code:
    >scaffold_1_length_46699537
    >scaffold_2_length_45526029
    >scaffold_3_length_45460755
    >scaffold_4_length_44284954
    >scaffold_5_length_43231337

    The first few lines of the gff look like this:
    Code:
    ##gff-version 3
    scaffold1_length_46699537       .       contig  1       46699537        .       .       .       ID=scaffold1_length_46699537;Name=scaffold1_length_46699537
    scaffold1_length_46699537       maker   gene    1701    4304    .       -       .       ID=Mlong585_00001;Name=Mlong585_00001;Alias=augustus-scaffold1_length_46699537-processed-gene-0.17;
    scaffold1_length_46699537       maker   mRNA    1701    4304    .       -       .       ID=Mlong585_00001-RA;Parent=Mlong585_00001;Name=Mlong585_00001-RA;Alias=augustus-scaffold1_length_46699537-processed-gene-0.17-mRNA-1;_AED=1.00
    scaffold1_length_46699537       maker   exon    1701    3837    .       -       .       ID=Mlong585_00001-RA:exon:78;Parent=Mlong585_00001-RA;
    scaffold1_length_46699537       maker   CDS     1701    3837    .       -       1       ID=Mlong585_00001-RA:cds;Parent=Mlong585_00001-RA;
    scaffold1_length_46699537       maker   exon    4012    4097    .       -       .       ID=Mlong585_00001-RA:exon:79;Parent=Mlong585_00001-RA;
    scaffold1_length_46699537       maker   CDS     4012    4097    .       -       0       ID=Mlong585_00001-RA:cds;Parent=Mlong585_00001-RA;
    scaffold1_length_46699537       maker   CDS     4173    4304    .       -       0       ID=Mlong585_00001-RA:cds;Parent=Mlong585_00001-RA;
    scaffold1_length_46699537       maker   exon    4173    4304    .       -       .       ID=Mlong585_00001-RA:exon:80;Parent=Mlong585_00001-RA;
    scaffold1_length_46699537       maker   gene    4819    8990    .       +       .       ID=Mlong585_00002;Name=Mlong585_00002;Alias=snap-scaffold1_length_46699537-processed-gene-0.25;
    scaffold1_length_46699537       maker   mRNA    4819    8990    .       +       .       ID=Mlong585_00002-RA;Parent=Mlong585_00002;Name=Mlong585_00002-RA;Alias=snap-scaffold1_length_46699537-processed-gene-0.25-mRNA-1;_AED=1.00;_QI
    scaffold1_length_46699537       maker   exon    4819    6558    .       +       .       ID=Mlong585_00002-RA:exon:48;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   CDS     4819    6558    .       +       0       ID=Mlong585_00002-RA:cds;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   CDS     7278    7432    .       +       0       ID=Mlong585_00002-RA:cds;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   exon    7278    7432    .       +       .       ID=Mlong585_00002-RA:exon:49;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   CDS     7462    7531    .       +       1       ID=Mlong585_00002-RA:cds;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   exon    7462    7531    .       +       .       ID=Mlong585_00002-RA:exon:50;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   CDS     7567    7629    .       +       0       ID=Mlong585_00002-RA:cds;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   exon    7567    7629    .       +       .       ID=Mlong585_00002-RA:exon:51;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   CDS     7639    7974    .       +       0       ID=Mlong585_00002-RA:cds;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   exon    7639    7974    .       +       .       ID=Mlong585_00002-RA:exon:52;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   CDS     8000    8056    .       +       0       ID=Mlong585_00002-RA:cds;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   exon    8000    8056    .       +       .       ID=Mlong585_00002-RA:exon:53;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   CDS     8800    8856    .       +       0       ID=Mlong585_00002-RA:cds;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   exon    8800    8856    .       +       .       ID=Mlong585_00002-RA:exon:54;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   CDS     8958    8990    .       +       0       ID=Mlong585_00002-RA:cds;Parent=Mlong585_00002-RA;
    scaffold1_length_46699537       maker   exon    8958    8990    .       +       .       ID=Mlong585_00002-RA:exon:55;Parent=Mlong585_00002-RA

Latest Articles

Collapse

  • seqadmin
    Quality Control Essentials for Next-Generation Sequencing Workflows
    by seqadmin




    Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

    Nucleic Acid Quality Control
    Preparing for NGS starts with isolating the...
    02-10-2025, 01:58 PM
  • seqadmin
    An Introduction to the Technologies Transforming Precision Medicine
    by seqadmin


    In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
    01-27-2025, 07:46 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-07-2025, 09:30 AM
0 responses
72 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-05-2025, 10:34 AM
0 responses
113 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-03-2025, 09:07 AM
0 responses
89 views
0 likes
Last Post seqadmin  
Started by seqadmin, 01-31-2025, 08:31 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Working...
X