Remember
"Computers are useless. They can only give you answers." — Pablo Picasso
What is this seq protocol? I've never heard of it!
my three-letter seq definition
Where can I learn more about sequencing or bioinformatics?
Short read sequencing anaysis by DnA lab (Dowell aNd Allen)
Differential expression of genes
Where can I find more about my favorite SNP(s)?
PhenVar-word cloud and network of papers for snps
Haploreg -connects snps to lots of data
Where can I find lists of genes that respond to stuff? Or lists of genes that are regulated by stuff?
GSEA Gene lists. List of genes that change in different conditions.
Can I find my favorite sequence in some other public data set?
Magic-BLAST. Blasts a fastq file… but don’t use it for big stuff. Its slow!
SearchSRA. You input a fasta file of a seq you care about (like a circlular RNA) and then you input a list of SRRs (samples from GEO) and it can give you back the reads that map against that fasta file from lots of geo samples.
Where can I learn more about my favorite gene?
(Like the expression level in a bunch of different cells types or the SNPs that regulate it, or that perturbations that change its expression, or what regulates my favorite gene)
TFs that regulate this gene (found via chip-seq database)
Where can I find data on my favorite TF?
GUI interface overlap chip-seq with public data (chip, sequence, annotation)
I did RNA-seq. I got a gene list. What do I do with my gene list? (warning: human or mouse)
Where can I find more stuff to read? (like you need more stuff to read)
Pubmed labs (this is googlefied pubmed searches)
How can I turn one cell type into another?
Where can I learn more about reproducibility and rigor and responsible conduct of research?