CAST/EiJ mouse strain Reference Transcriptome (do we have one? if not, how to build?)

Question

[Rhodnius]

Hi Everybody,

I hope you are doing OK during this time.

I'm curious if someone knows the existence of a reference transcriptome for CAST/EiJ mouse strain or if anyone knows how to build from scratch (That even applies for the other "founder" strains such as 129S1, NOD, NZO, PWK, and WBS (considering that we already have for C57BL/6).

I need that reference transcriptome for quantifying an RNAseq experiment using Salmon.

I've been looking for that information for a while, but I didn't find anything conclusive.

I appreciate any insight/suggestions.

Thanks a lot and have a lovely week,

Juan C.S. Arcila.

Answer 1

[mark.ziemann]

If you visit the Ensembl FTP site [1] and search for "CAST/EiJ" you will see there is a build for this strain. Similarly there are many other mouse strains also included. The "cDNA" fasta can be used for Salmon and Kallisto. Just take note that this will not include non-coding RNAs. I you want those as well, you will need to concatenate the two FASTA files before indexing.

1. http://asia.ensembl.org/info/data/ftp/index.html