HISAT2 indexes, GRCm38 or mm10?

Question

[Buffo]

Hi everybody,

Somebody knows which is the difference between GRCM38 and mm10 genomes? There are both HISAT2 indexes. Which is the difference?

Thanks

[GenoMax]

mm10 is likely UCSC version of the genome. GRCh38 is from Genome Reference Consortium (NCBI). UCSC version will have chr* identifiers. Sequence should be identical in both cases for main chromosomes.

Answer 1

[Sej Modha]

Just different versions of the genome indexes. GRC - Genome Reference Consortium - https://www.ncbi.nlm.nih.gov/grc/mouse UCSC - http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgGateway?db=mm10

Answer 2

[iraia.munoa]

Hi everyone,

I add here my question, because it is about both GRCm38 and mm10 reference genomes.

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 analysis (the alingment). I think the correct one will be the GRCm38, but 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