gireeshkbogu

# see below for UPDATES that include more shorter ways of conversions

# How to convert GTF format into BED12 format (Human-hg19)?
# How to convert GTF or BED format into BIGBED format?
# Why BIGBED (If GTF or BED file is very large to upload in UCSC, you can use trackHubs. However trackHubs do not accept either of the formats. Therefore you would need bigBed format)

# First, download UCSC scripts
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToBed
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed

fabiovalse

A node-link diagram running a javascript implementation of the Dijkstra algorithm. Every time the visualization is refreshed two nodes are selected as start (in red) and end point (in blue). Then the shortest path is computed and shown on the diagram by highlighting the edges.

MadLittleMods

Just some notes and references for myself.

• In bash, you can access your C:\ drive via /mnt/c/
• ~ = C:\Users\MLM\AppData\Local\lxss\home\mlm and is different from your Windows user directory C:\Users\MLM

How to google things

runspired

var lastFlushed = undefined;

function floodScheduler(n) {
  for (var i = 0; i < 10; i++) {
    for (var j = 0; j < n; j++) {
      var fn = function logPos(i, j) {
        var thisFlush = (i * n) + j;
        if (lastFlushed || lastFlushed === 0) {
          if (lastFlushed + 1 !== thisFlush) {
            console.error('Order MisMatch', lastFlushed, thisFlush, i, j);

sestaton

fmtDetailValue_Dbxref : function(dbxref) { 
    if (typeof dbxref != 'string') { 
        return dbxref;
    } 
    var dbid = dbxref.split(':'); 
    var prefix = ''; 
    switch (dbid[0]) { 
      case 'InterPro': 
        prefix = 'http://www.ebi.ac.uk/interpro/entry/'; 
        break; 

jexp

export NEO4J_HOME=${NEO4J_HOME-~/Downloads/neo4j-community-3.0.1}

if [ ! -f data-csv.zip ]; then
  curl -OL https://cloudfront-files-1.publicintegrity.org/offshoreleaks/data-csv.zip
fi
	
export DATA=${PWD}/import

rm -rf $DATA

lh3

Source	Dst. file type	Protocol	Time (s)	Command Line
NCBI	.sra	ftp	296	wget
NCBI	.fastq.gz	sra toolkit	~23000	fastq-dump -Z --gzip --split-spot
local file	sra=>fastq.gz	sra toolkit	~15000	fastq-dump --gzip --split-spot --split-3
EBI	.fastq.gz	aspera	513+492	aspera -QT -l 300m
EBI	.fastq.gz	ftp	1876+1946	wget

Notes:

superbobry

TDF

TDF is a binary format developed by the IGV team at Broad Institute.

Overview

Concepts

alphapapa

#!/bin/bash

less_command='| less $less_no_init -aiF -Ps"Manual page\: $man_page (?ltline %lt?L/%L.:byte %bB?s/%s..? (END):?pB %pB\%..)"'

# Get section
if [[ $1 =~ [0-9]+ ]]
then
    section=$1
    shift
fi

audy

#!/bin/bash

export PATH='/usr/local/bin:$PATH'

ansiweather -a off -l 'San Francisco' \
  | cut -d '>' -f 2 \
  | cut -d '-' -f1 \
  | awk '{ print $1 $2 }' \
  | tr -d 'C'