anamariaelek

BAM=$1
SAM=${BAM%.bam}.sam
BAMCB=${BAM%.bam}.CB.bam
BAMCBSORT=${BAM%.bam}.CB.sorted.bam
BAMNFR=${BAM%%.bam}.CB.NFR.bam
BAMNFRSORT=${BAM%%.bam}.CB.NFR.sorted.bam
FRAGMENTS=${BAMNFRSORT%.bam}.fragments
NCORES=$2

echo "Adding CB tag to" $BAM

anamariaelek

# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
#                           GLOBAL                          # 
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #  

if (!require(shiny)) install.packages("shiny")
if (!require(shinydashboard)) install.packages("shinydashboard")
require(shiny)
require(shinydashboard)
require(stringr)
require(data.table)

anamariaelek

#!/usr/bin/env python
#-*- coding: utf-8 -*-

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of

anamariaelek

#!/bin/bash

# find interesting articles PMIDs
db='pubmed'
query='Metagenome[mesh]+AND+Gastrointestinal+Microbiome[mesh]+AND+2008:2018[pdat]+AND+Journal+Article[ptyp]'
base='https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
url=$base"esearch.fcgi?db=$db&term=$query&retmax=100000"
curl $url -g -o esearch_pmid.xml

# save list of PMIDs to a text file

anamariaelek

require(shiny)
require(shinydashboard)
require(data.table)
require(ggplot2)
require(ggpubr)
require(stringr)
require(DT)
require(kableExtra)
require(knitr)
require(plotly)