Tabea Kischka Tabea-K

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crtl + shift + R

Filter	Description
alt_allele_in_normal	Evidence seen in the normal sample
clustered_events	Clustered events observed in the tumor
germline_risk	Evidence indicates this site is germline, not somatic
homologous_mapping_event	More than three events were observed in the tumor
multi_event_alt_allele_in_normal	Multiple events observed in tumor and normal
panel_of_normals	Seen in at least 2 samples in the panel of normals

Die Datei seq.fasta muss immer auf dem Desktop liegen!

um die header Zeilen zu entfernen:

grep -v ">" ~/Desktop/seq.fasta > ~/Desktop/seq_ohne_header.fasta

Run using the command pdflatex test.tex

An overleaf document can be found here: https://www.overleaf.com/read/tynwkrwwpfmk When you click on the link you can also the resulting PDF

	#!/bin/bash
	# This small script can set the exif metadata of a jpeg file
	# to the date and time given in the file name assigned by WhatsApp
	# when downloading the image.
	# The filename needs to be in a format like this (the automatically assigned
	# format as of 2019-02-12):
	# "WhatsApp Image 2018-09-20 at 17.18.42.jpeg"

	# In order to modify all jpeg files in a folder,
	# run the command like this:

	CURRDATE=`date +%Y-%m-%d`
	ASSEMBLY=hg38
	mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D "${ASSEMBLY}" -e "select * \
	from refGene" > "${CURRDATE}_${ASSEMBLY}_refGene.txt"

	#!/usr/bin/python

	from Bio import Entrez

	Entrez.email = '[email protected]'

	def get_gene_info(refseq_id):
	"""
	Queries the ncbi refseq database for the gene summary
	"""

	#!/bin/bash
	# This creates a more or less empty template for a python package
	# containing unit tests
	# Author: Tabea Kischka, 2018-07-02
	# Version 2.0, last update: 2018-08-28

	###########################################################################################################
	# get options
	###########################################################################################################

	GIMP Palette
	Name: colorblind_grayscale
	Columns: 3
	# Based on http://jfly.iam.u-tokyo.ac.jp/color/image/pallete.jpg
	0 0 0 seq_OrRd_4_01
	42 42 42 seq_OrRd_4_01
	165 165 165 seq_OrRd_4_02
	230 159 0 seq_OrRd_4_02
	167 167 167 seq_OrRd_4_03
	86 180 233 seq_OrRd_4_03