Differences Between Ensembl, Gencode, RefSeq and UCSC

Cited from "Question: Difference Between Ensembl Databases In Ucsc Table Browser"

"Vega is a browser of the manually curated Havana gene set. Ensembl also perform automatic annotation of genes using protein and nucleotide sequence databases, such as EMBL, Uniprot and RefSeq. Ensembl use the GENCODE gene set, which is made up of the Havana and Ensembl automatic gene set. Genes within the GENCODE set are labelled as being either Ensembl (from the automatic annotation), Havana (from the manual annotation) or merged (exact match between the automatic and manual annotation)."
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Retrieve UCSC mm9.fa

MeQA: A pipeline for MeDIP-seq data quality assessment and analysis

Awk: Built-in Variables

8 Powerful Awk Built-in Variables – FS, OFS, RS, ORS, NR, NF, FILENAME, FNR

Convert BedGraph to Bed

Question: Bedgraph To Bed

Bash: Create a Temporary Directory

How to create a temporary directory?

Awk: Split a File Into Multiple Files

awk - 10 examples to split a file into multiple files

efficiently splitting one file into several files by value of column

R EOF

Cited from R Command Line Processing

cat > printargs.R << EOF args = commandArgs() print(args) q() EOF

R --no-save < printargs.R

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CLIP-seq Analysis Tools

An integrative resource of CLIP-seq studies

CLIPper-Home

RIP-seq/CLIP-seq software tools

CLIP-seq Analysis Example Papers

Transcriptome-wide identification of RNA binding sites by CLIP-seq

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins

Bash PS Command

The ps Command

Bash the Difference Between PATH and LD_LIBRARY_PATH

What is the difference between PATH and LD_LIBRARY_PATH?

Bash Indirect Expansion

bash: indirect expansion, please explain?

Bash: Substring Removal

Cited from "How do I parse command line arguments in bash?"

To better understand ${i#*=} search for "Substring Removal" in this guide. It is functionally equivalent to `sed 's/[^=]*=//' <<< "$i"` which calls a needless subprocess or `echo "$i" | sed 's/[^=]*=//'` which calls two needless subprocesses.

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Bash Command: Xargs

10 Xargs Command Examples in Linux / UNIX

Safe and powerful use of xargs with bash and grep

Things you (probably) didn’t know about xargs

4C-seq Protocol and Primer Design

Robust 4C-seq data analysis to screen for regulatory DNA interactions

4C Primer Designer for 4C Viewpoints

4C-Seq primer database

Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method

The high-resolution 4C-seq method and the iterative correction procedure for Hi-C data.

4C Analysis Tools

Basic4Cseq: an R/Bioconductor package for the analysis of 4C-seq data

4Cseqpipe

FourCSeq: Analysis of 4C sequencing data

Message Passing

Cited from OO field guide

"With message-passing, messages (methods) are sent to objects and the object determines which function to call."

Function Names With Leading Dots

Cited from What does the dot mean in R – personal preference, naming convention or more?

"Function names with leading dots are somewhat hidden from general view. Functions that are meant to be purely internal to a package sometimes use this.

In this context, "somewhat hidden" simply means that the variable (or function) won't normally show up when you list object with ls(). To force ls to show these variables, use ls(all.names=TRUE). By using a dot as first letter of a variable, you change the scope of the variable itself. "