star alignment FVB mouse reference genome

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Γεωργία Γιωτοπούλου

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Dec 1, 2021, 5:38:34 PM12/1/21
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Dear all,

I am trying to analyze RNA seq data from FVB murine lung tumors, produced using the HiSeq 4000 platform (Illumina) as paired-end 150 bp reads. I aligned the sequencing reads to the mm9 (MGSCv37, NCBI build M37) version of Mus musculus genome using STAR2.7.3a. However, I am concerned because the mm9 reference corresponds to C57Bl/6 mouse genome and unfortunately I have not found any FVB mouse reference genome available for using with STAR.

I would really appreciate your help,
Best,
Georgia

Alexander Dobin

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Dec 3, 2021, 2:20:43 PM12/3/21
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Hi Georgia,

what are the mapping stats in the Log.final.out?
If the mapping rate is not too low and error rates not too high, you can likely use the alignments.

Cheers
Alex

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