kallisto transcriptome website is down

[alfonsosaera]

Hi,

I am following the getting started tutorial (http://pachterlab.github.io/kallisto/10xstarting.html) for single cell RNAseq but when I get to the point:

Download the “human-mouse” transcriptome from the kallisto transcriptome website.

I cannot access the link (http://pachterlab.github.io/kallisto/transcriptomes/), I get the following message:

Sorry this page does not exist =(

Could you direct me to the right website? alternatively, could you describe the "human-mouse" transcriptome file?

Thanks!!

[biostat0903]

I got the same issue, how can I get this file?

[nkimoto]

@alfonsosaera @biostat0903
You can get the fasta files from
ftp://ftp.ensembl.org/pub/current_fasta/

and merge files to one fasta file like below.

# Download and merge human cDNA and ncDNA files from Ensembl for the index.
wget ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
wget ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz

# Download and merge Mus_musculus cDNA and ncDNA files from Ensembl for the index.
wget ftp://ftp.ensembl.org/pub/current_fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
wget ftp://ftp.ensembl.org/pub/current_fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz

# Merge human and Mus_musculus fasta files.
cat Homo_sapiens.GRCh38.cdna.all.fa.gz Homo_sapiens.GRCh38.ncrna.fa.gz Mus_musculus.GRCm38.ncrna.fa.gz Mus_musculus.GRCm38.cdna.all.fa.gz > Mus_musculus.GRCm38_Homo_sapiens.GRCh38.cdna.mix.fa.gz