Question: CAST/EiJ mouse strain Reference Transcriptome (do we have one? if not, how to build?)
0
gravatar for Rhodnius
4 weeks ago by
Rhodnius0
Rhodnius0 wrote:

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.

transcriptome salmon cast mouse • 117 views
ADD COMMENTlink modified 4 weeks ago by mark.ziemann1.3k • written 4 weeks ago by Rhodnius0
1
gravatar for mark.ziemann
4 weeks ago by
mark.ziemann1.3k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.3k wrote:

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
ADD COMMENTlink written 4 weeks ago by mark.ziemann1.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1569 users visited in the last hour