# salmon quantmerge giving fewer rows than expected

**URL:** https://help.galaxyproject.org/t/salmon-quantmerge-giving-fewer-rows-than-expected/7130
**Category:** usegalaxy.eu support
**Tags:** salmon
**Created:** [December 1, 2021, 11:26am UTC](https://help.galaxyproject.org/t/salmon-quantmerge-giving-fewer-rows-than-expected/7130 "2021-12-01T11:26:36Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![Mark\_J\_Dunning](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mark_j_dunning/32/2875_2.png) [@Mark\_J\_Dunning](https://help.galaxyproject.org/u/Mark_J_Dunning)
#### Post date: [December 1, 2021, 11:26am UTC](https://help.galaxyproject.org/t/salmon-quantmerge-giving-fewer-rows-than-expected/7130/1 "2021-12-01T11:26:36Z")

</div>

Hi,

I have used salmon quant on a series of samples, and would like to merge the raw counts into a matrix for further processing. I have used a transcript-to-gene mapping file to get gene-level quantifications.

Each of my gene quantification outputs has 38,175 rows, but when I use quantmerge I only get 979 rows.

In quantmerge, I selected my gene quantification outputs and the NumReads column to merge.

I didn’t know whether to tick the Genes button or not. If I tick it, I get 0 rows in the quantmerge output.

Is there something I’m not understanding about this tool?

Could I use a column join instead to merge the data?

Thanks,

Mark