text: user7331: (Ported from stack overflow)
  I'm trying to summarize gene count using htseq-count; and it's returning 0 counts at every gene. I'm not sure what I'm doing wrong; I think it has to do with the gene flag I'm using. 
  I've tried using the GTF for Arabidopsis TAIR 10: which I got from: ftp://ftp.ensemblgenomes.org/pub/release-46/plants/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.46.gtf.gz as well as the GFF file available on Araport.
  I'm using various BAM files I know to have gene expression values.
  I've tried both locally and on galaxy
  The local commands I've tried so far are:
  python3 -m HTSeq.scripts.count --idattr=gene_id #bam #gtf > summary.txt
  python3 -m HTSeq.scripts.count -i gene_id #bam #gff > summary.txt
  python3 -m HTSeq.scripts.count -i locus_tag #bam #gff > summary.txt
  python3 -m HTSeq.scripts.count -i ID #bam #gff > summary.txt
  python3 -m HTSeq.scripts.count -i SeqID #bam #gff > summary.txt
  python3 -m HTSeq.scripts.count -i Parent #bam #gff > summary.txt
  
  I've done the same on galaxy; inputing the -i value in.
  Any help as to where I'm going wrong would be great.
  Thanks!
  
  user6955: Maybe the contig names in your BAM files don't match those in the GFF file? Ensembl uses contig names like 1, some other reference sources use chr1. 
  Generally, for ensembl GFF files, HTSeq's default value for idattr should be fine though.
  
original_text: 7331: <p>(Ported from stack overflow)</p>
  
  <p>I'm trying to summarize gene count using htseq-count; and it's returning 0 counts at every gene. I'm not sure what I'm doing wrong; I think it has to do with the gene flag I'm using. 
  I've tried using the GTF for Arabidopsis TAIR 10: which I got from: <a href="ftp://ftp.ensemblgenomes.org/pub/release-46/plants/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.46.gtf.gz" rel="nofollow noreferrer">ftp://ftp.ensemblgenomes.org/pub/release-46/plants/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.46.gtf.gz</a> as well as the GFF file available on Araport.</p>
  
  <p>I'm using various BAM files I know to have gene expression values.</p>
  
  <p>I've tried both locally and on galaxy
  The local commands I've tried so far are:</p>
  
  <pre><code>python3 -m HTSeq.scripts.count --idattr=gene_id #bam #gtf &gt; summary.txt
  python3 -m HTSeq.scripts.count -i gene_id #bam #gff &gt; summary.txt
  python3 -m HTSeq.scripts.count -i locus_tag #bam #gff &gt; summary.txt
  python3 -m HTSeq.scripts.count -i ID #bam #gff &gt; summary.txt
  python3 -m HTSeq.scripts.count -i SeqID #bam #gff &gt; summary.txt
  python3 -m HTSeq.scripts.count -i Parent #bam #gff &gt; summary.txt
  </code></pre>
  
  <p>I've done the same on galaxy; inputing the -i value in.</p>
  
  <p>Any help as to where I'm going wrong would be great.</p>
  
  <p>Thanks!</p>
   6955: <p>Maybe the contig names in your BAM files don't match those in the GFF file? Ensembl uses contig names like <code>1</code>, some other reference sources use <code>chr1</code>. </p>
  
  <p>Generally, for ensembl GFF files, HTSeq's default value for idattr should be fine though.</p>
  