# I was trying to count the number of reads through HTSeq but failed.

**URL:** <https://help.galaxyproject.org/t/i-was-trying-to-count-the-number-of-reads-through-htseq-but-failed/337>\
**Category:** Uncategorized\
**Created:** [January 7, 2019, 7:58am UTC](https://help.galaxyproject.org/t/i-was-trying-to-count-the-number-of-reads-through-htseq-but-failed/337 "2019-01-07T07:58:21Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Raja\_ishaq\_Nabi\_Khan](https://avatars.discourse-cdn.com/v4/letter/r/22d042/32.png) [@Raja\_ishaq\_Nabi\_Khan](https://help.galaxyproject.org/u/Raja_ishaq_Nabi_Khan)\
**Post date:** [January 7, 2019, 7:58am UTC](https://help.galaxyproject.org/t/i-was-trying-to-count-the-number-of-reads-through-htseq-but-failed/337/1 "2019-01-07T07:58:22Z")

</div>

The results of HTSeq is shown in plain image . What could be reason for this ?? Erroneous Gff file or erroneous Bam file? I am attaching here sorted report of the bam file ( green background) as well

![45%20PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/1X/c27d4a0943227556e18bdee1f162e92f484041b0.png) ![22%20PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/1X/78e2e5f8b263f1200bea7327b1d9aa6c2774735a.png)

---

<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [January 7, 2019, 5:06pm UTC](https://help.galaxyproject.org/t/i-was-trying-to-count-the-number-of-reads-through-htseq-but-failed/337/2 "2019-01-07T17:06:48Z")

</div>

Does the GTF dataset contain any data lines with “exon” in the 3rd column? The error suggest that it doesn’t and you either need to modify the feature used for counting or find a more suitable GTF source.

Exon is the default feature considered by HTseq-count wrapped for Galaxy. Screenshot:

 ![htseq-feature-default](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/1X/1510461dc9bb7222963dece7311ec7d234e98fd1.png)

Please see the RNA-seq tutorials for example usage:

> [@](#):
>
> [Galaxy Training Network Tutorials](https://galaxyproject.github.io/training-material/): Some [GTN](https://galaxyproject.org/teach/gtn/) tutorials are appropriate for [Galaxy Main](https://usegalaxy.org) and some are not. Where you can run each is noted per tutorial – click on the _Galaxy instances_ gear icon ![galaxyserversGTN](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/1X/1287f50cfcdaa1aad750fe323f96995260ac4947.png) to review the [Public Galaxy](https://galaxyproject.org/use/) server choices. If a tutorial is supported by a pre-configured [Galaxy Docker](https://hub.docker.com/r/bgruening/galaxy-stable/) training image, instructions for how to get it will be listed below the tutorial listings, per category.

Support FAQs:

- [My job ended with an error. What can I do?](https://galaxyproject.org/support/tool-error/)
- [Common datatypes explained](https://galaxyproject.org/learn/datatypes/)