# Extracting RNA-count data for specific genes from expression matrix

**URL:** https://community.brain-map.org/t/extracting-rna-count-data-for-specific-genes-from-expression-matrix/511
**Category:** Technical
**Tags:** transcriptomics, rna-seq, how-to
**Created:** [April 15, 2020, 9:34am UTC](https://community.brain-map.org/t/extracting-rna-count-data-for-specific-genes-from-expression-matrix/511 "2020-04-15T09:34:33Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![jeremyinseattle](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/jeremyinseattle/32/50_2.png) [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)
#### Post date: [April 15, 2020, 4:15pm UTC](https://community.brain-map.org/t/extracting-rna-count-data-for-specific-genes-from-expression-matrix/511/2 "2020-04-15T16:15:36Z")

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Hi @A_Muc. The recommended way to read this file using R is written in the [.readme](https://brainmapportal-live-4cc80a57cd6e400d854-f7fdcae.divio-media.net/filer_public/1f/5e/1f5ed635-ab00-4abd-9518-720a83a5768d/readme_mouse.txt). In particular, the `read_tome_gene_data` function in the [scrattch.io](https://github.com/AllenInstitute/scrattch.io) R package will be useful. If you prefer using python, please see [this forum post](https://community.brain-map.org/t/loading-data-from-transcrip-tome-file-in-python-with-h5py/310).

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