Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • htseq-count error

    Hello,

    I am trying to use htseq-count as follows:
    htseq-count bin2_s_7_bwa.sam Mycobacterium_bovis_BCG_Pasteur_1173P2.gff

    But I get the following error:
    Error occured in line 10 of file /mnt/ScratchPool/rouamsl/TB_sequencing/ReadCount/Mycobacterium_bovis_BCG_Pasteur_1173P2.gff.
    Error: The attribute string seems to contain mismatched quotes.
    [Exception type: ValueError, raised in __init__.py:168]

    My .gff file looks like this:
    ##gff-version 3
    #!gff-spec-version 1.20
    #!processor NCBI annotwriter
    ##sequence-region NC_008769.1 1 4374522
    ##species http://www.ncbi.nlm.nih.gov/Taxonomy....cgi?id=410289
    ##sequence-region NC_008769.1 1 4374522
    ##species http://www.ncbi.nlm.nih.gov/Taxonomy....cgi?id=410289
    NC_008769.1 RefSeq region 1 4374522 . + . ID=id0;Dbxref="taxon:410289";Is_circular=true;gbkey=Src;genome=chromosome;mol_type="genomic DNA";strain="BCG Pasteur 1173P2"
    NC_008769.1 RefSeq gene 1 1524 . + . ID=gene0;Name=dnaA;Dbxref="GeneID:4697358";gbkey=Gene;gene=dnaA;locus_tag=BCG_0001
    NC_008769.1 RefSeq CDS 1 1524 . + 0 ID=cds0;Name=YP_976107.1;Parent=gene0;Note="binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.";Dbxref="GeneID:4697358","GI:121635884";gbkey=CDS;product=YP_976107.1;protein_id=YP_976107.1;transl_table=11

    I found a similar post on the forum at
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

    But it was not solved! And it was using gtf files (and not gff).

    I downloaded my .gff file as follows (from the NCBI website):
    wget --timestamping 'ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Mycobacterium_bovis_BCG_Pasteur_1173P2_uid58781/NC_008769.gff' -O Mycobacterium_bovis_BCG_Pasteur_1173P2.gff

    Thank you for your help!

    Regards,
    S

Latest Articles

Collapse

  • 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
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-27-2024, 06:37 PM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X