Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-06T10:11:13.900Z
Answers.LastActivityDate: 2020-03-06T10:11:13.900Z
Answers.UserDisplayName: DavyCats
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-06T14:09:05.800Z
Comments.Text: hey @sdshinghal, check a few things. 1. ensure bam file is ok (you can look at it), 2. like the answer below, check your gtf matches the reference genome
Comments.UserDisplayName: StupidWolf
Tags: <sam><gene><gene-expression><gff>
Title: HTSeq-count is returning 0 for every gene, instead of expression value
ThreadText: # HTSeq-count is returning 0 for every gene, instead of expression value
  
  (Asked by: username_0 on 2020-03-06)
  
  (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!
  
  **Tags:** sam, gene, gene-expression, gff
  
  > **Comments:**
  > **username_1**: hey @username_0, check a few things. 1. ensure bam file is ok (you can look at it), 2. like the answer below, check your gtf matches the reference genome  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-03-06. Score: 1
  
  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.
  
  
  ---
  
  