diff --git a/docs/getting_started/Tutorial.rst b/docs/getting_started/Tutorial.rst index 494d834..d0543fc 100644 --- a/docs/getting_started/Tutorial.rst +++ b/docs/getting_started/Tutorial.rst @@ -27,11 +27,15 @@ Tutorial start mkdir count cd count - wget https://datashare.molbiol.ox.ac.uk/public/project/cribbslab/acribbs/Trimer/test.fastq.gz - wget https://datashare.molbiol.ox.ac.uk/public/project/cribbslab/acribbs/Trimer/Homo_sapiens.GRCh38.cdna.all.fa - wget https://datashare.molbiol.ox.ac.uk/public/project/cribbslab/acribbs/Trimer/hg38.fa - wget https://datashare.molbiol.ox.ac.uk/public/project/cribbslab/acribbs/Trimer/hg38_geneset_all.bed - wget https://datashare.molbiol.ox.ac.uk/public/project/cribbslab/acribbs/Trimer/hg38_geneset_all.gtf + wget https://ftp.ensembl.org/pub/release-113/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz + wget https://datashare.molbiol.ox.ac.uk/public/project/cribbslab/acribbs/tallytrin_tutorial/hg38.fasta + wget https://datashare.molbiol.ox.ac.uk/public/project/cribbslab/acribbs/tallytrin_tutorial/geneset_all.bed + wget https://datashare.molbiol.ox.ac.uk/public/project/cribbslab/acribbs/tallytrin_tutorial/geneset_all.gtf.gz + + gunzip geneset_all.gtf.gz + gunzip Homo_sapiens.GRCh38.cdna.all.fa.gz + +You will need to download the test data file from GEO using sra-toolkit (https://github.com/ncbi/sra-tools) here: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRX18398120&o=acc_s%3Aa **2.** Next we will generate a configuration yml file so the pipeline output can be modified:: @@ -58,7 +62,7 @@ this case:: cdna_fasta: Homo_sapiens.GRCh38.cdna.all.fa - genome_fasta: hg38.fa + genome_fasta: hg38.fasta junc_bed: hg38_geneset_all.bed