search

xie186 / miscellaneous_note

0 stars 0 forks source link

prepare mm10 for VIPER #14

Open xie186 opened 4 years ago

xie186 commented 4 years ago

VIPER provided index information for 

mkdir VIPER_static/mm10/assembly/
xie186 commented 4 years ago

Annotation

ENSEMBL Biomart

Gene stable ID Gene stable ID version Gene name GO term accession GO term name
xie186 commented 4 years ago

Donwload genome

Primary assembly vs Top level?

http://genomespot.blogspot.com/2015/06/mapping-ngs-data-which-genome-version.html

wget ftp://ftp.ensembl.org/pub/release-97/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-97/gtf/mus_musculus/Mus_musculus.GRCm38.97.gtf.gz
gunzip Mus_musculus.GRCm38.97.gtf.gz
module load bioinfo STAR
STAR   --runMode genomeGenerate   --runThreadN 24   --genomeDir STAR_rRNA/   --genomeFastaFiles Mus_musculus.GRCm38.ncrna.fa --limitGenomeGenerateRAM 45000000000
xie186 commented 4 years ago

rRNA for mm9

image

xie186 commented 4 years ago

FAQ:

/depot/bioinfo/data/Projects/Shannahan/toxicity_RNAseq/results/viper_project/.snakemake/conda/fae5cabf/lib/R/bin/R: line 238: /depot/bioinfo/data/Projects/Shannahan/toxicity_RNAseq/results/viper_project/.snakemake/conda/fae5cabf/lib/R/etc/ldpaths: No such file or directory
Waiting at most 5 seconds for missing files.
MissingOutputException in line 91 of /depot/bioinfo/data/Projects/Shannahan/toxicity_RNAseq/results/viper_project/viper/modules/readQC.snakefile:
Missing files after 5 seconds:
analysis/RSeQC/junction_saturation/HS3h2/HS3h2.junctionSaturation_plot.pdf
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.

conda ldpaths: no such file or directory

cp /scratch/halstead/x/xie186/zhulab/RNA-seq/viper/envs/.viper/lib/R/etc/ldpaths /depot/bioinfo/data/Projects/Shannahan/toxicity_RNAseq/results/viper_project/.snakemake/conda/fae5cabf/lib/R/etc/ldpaths