Mouse transcriptome contaminant removal

Infrastructure and utilities KneadData
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Is there a precompiled index for the mouse transcriptome like there is the human transcriptome that can be utilized for contaminant removal?

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Hi @jbarlow ,

We do have the mouse Strain C57BL_6NJ available at the moment: http://huttenhower.sph.harvard.edu/kneadData_databases/mouse_C57BL_6NJ_Bowtie2_v0.1.tar.gz. Let me know if this helps.

Regards,
Sagun

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Hi Sagun,

Thanks for the reply. I am aware of the C57BL_6NJ reference database. I am currently using this and it is working fine. Correct me if I’m wrong, but I assume this is for the genome and thus would be missing any splice variants etc that would only be in the transcriptome. That’s why I was curious if there was also a mouse transcriptome reference similar to how there is both a human genome and transcriptome reference.