Database

bwa genome index

BWAINDEX_hg19$ bwa index -a bwtsw /home/reference/hg19.fa 

hg19.bed

https://www.biostars.org/p/80443/

How to get data from a paper:

NCBI GEO(peaks)

SRA(raw fastq)

EBL-EBI(processed bam file using paper name)

https://www.ebi.ac.uk/

COSMIC(RNA-seq/gene expression data for each cell line)

https://cancer.sanger.ac.uk/cosmic/download

 

TCGA cancer types

https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations

Epigenome Atlas expression data

https://egg2.wustl.edu/roadmap/web_portal/processed_data.html#RNAseq_uni_proc