# Influence of different reference genomes used for mapping

**URL:** <https://discourse.scverse.org/t/influence-of-different-reference-genomes-used-for-mapping/435>\
**Category:** scanpy\
**Created:** [May 4, 2022, 8:46pm UTC](https://discourse.scverse.org/t/influence-of-different-reference-genomes-used-for-mapping/435 "2022-05-04T20:46:50Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![auesro](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/auesro/32/216_2.png) [@auesro](https://discourse.scverse.org/u/auesro)\
**Post date:** [May 4, 2022, 8:46pm UTC](https://discourse.scverse.org/t/influence-of-different-reference-genomes-used-for-mapping/435/1 "2022-05-04T20:46:50Z")

</div>

I am trying to integrate 2 scRNAseq datasets: one previously published where the authors used the refdata-cellranger-mm10-1.2.0 reference in Cell Ranger, and one I have generated where I used the refdata-gex-mm10-2020-A reference in Cell Ranger.

I was wondering what would be the better approach to tackle this problem. Is it important for the integration process? How should I approach the analysis? Is it possible to convert their gene names to mines? Do I have to re-align my reads to the same reference files used by the other lab?

Looking forward to your ideas!