# Metatranscriptomic pre-processing

**URL:** <https://forum.biobakery.org/t/metatranscriptomic-pre-processing/5608>\
**Category:** bioBakery workflows\
**Created:** [July 6, 2023, 3:36pm UTC](https://forum.biobakery.org/t/metatranscriptomic-pre-processing/5608 "2023-07-06T15:36:35Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![garfield](https://avatars.discourse-cdn.com/v4/letter/g/46a35a/32.png) [@garfield](https://forum.biobakery.org/u/garfield)\
**Post date:** [July 6, 2023, 3:36pm UTC](https://forum.biobakery.org/t/metatranscriptomic-pre-processing/5608/1 "2023-07-06T15:36:35Z")

</div>

Hi, can I use “wmgx” workflow (change --contaminate-databases) to analyze metatranscriptomic data? I already got the taxonomic and functional profiling from metagenomes and would like to skip this process in " wmgx\_wmtx".

Also, do you know how to include 2 types of contaminate databases (e.g., human transcriptome and ribosomal RNA) when running “biobakery\_workflows wmgx”? I tried to add two “–contaminate-databases” but only the last database was used.

---

<div class="post-metadata">

**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [July 21, 2023, 3:45pm UTC](https://forum.biobakery.org/t/metatranscriptomic-pre-processing/5608/2 "2023-07-21T15:45:06Z")

</div>

Hi, Yes you can do that. To include 2 databases provide them in a comma-delimited list.

Thank you,  
Lauren

---

<div class="post-metadata">

**Author:** ![Jaydee](https://avatars.discourse-cdn.com/v4/letter/j/ee7513/32.png) [@Jaydee](https://forum.biobakery.org/u/Jaydee)\
**Post date:** [May 30, 2024, 12:38am UTC](https://forum.biobakery.org/t/metatranscriptomic-pre-processing/5608/3 "2024-05-30T00:38:22Z")

</div>

@lauren.j.mciver @franzosa

This is an excellent workaround. I made it to work but raised a question in my mind.

As far as I understood, running wmgx\_wmtx workflow helps profiling species content from DNA when we try to map the RNA reads. In this case, we only run wmtx. How does it work? Can we still extract functional activity from the outputs of this cool workaround?

P.S. If we are not focusing on relative contributions to mgx/mtx, viral profiling could be a good application.

---

<div class="post-metadata">

**Author:** ![Jaydee](https://avatars.discourse-cdn.com/v4/letter/j/ee7513/32.png) [@Jaydee](https://forum.biobakery.org/u/Jaydee)\
**Post date:** [June 13, 2024, 6:05pm UTC](https://forum.biobakery.org/t/metatranscriptomic-pre-processing/5608/4 "2024-06-13T18:05:30Z")

</div>

@lauren.j.mciver May I know how does the profiling work in this case please?