GRCm38 and mm10 reference genomes, Which one to use?

iramai · 05-26-2020, 06:43 AM

Hy everybody!
I have received the fastq files of some Bisulfite sequencing samples. For the sequencing they have used "gem3.mmusculus.GRCm38_BS" as a reference. But I am not sure what genome to use for the alingment(the GRCm38 or the mm10 from the UCSC), because I have other older RNA sequences anayzed with the mm10 reference genome, and I would like to compare both of them in the future.
- Is it posible to compare some sequences with the GRC38 genome and others with the mm10 genome, for example at the UCSC genome browser (with the bedgraph files I mean)?
- Is there a way to change something in the fastq files of the bisulfite sequencing for example to finally do the alignment with the mm10 reference genome?

Thanks in advance,

Iraia

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05-26-2020, 06:43 AM	#1
iramai Junior Member Location: Eibar Join Date: Mar 2018 Posts: 6	GRCm38 and mm10 reference genomes, Which one to use? Hy everybody! I have received the fastq files of some Bisulfite sequencing samples. For the sequencing they have used "gem3.mmusculus.GRCm38_BS" as a reference. But I am not sure what genome to use for the alingment(the GRCm38 or the mm10 from the UCSC), because I have other older RNA sequences anayzed with the mm10 reference genome, and I would like to compare both of them in the future. - Is it posible to compare some sequences with the GRC38 genome and others with the mm10 genome, for example at the UCSC genome browser (with the bedgraph files I mean)? - Is there a way to change something in the fastq files of the bisulfite sequencing for example to finally do the alignment with the mm10 reference genome? Thanks in advance, Iraia