download as pdf How to set up infrastructure for ChIP-seq analysis using the Biostars Handbook 2nd edition according to Ming Tangs Guide. Setting up the folder structure Go to the directory for ChIP-seq with your analysis cd ~/work/ChIP-seq_<analysis-name> mkdir {data,results,scripts,software} mkdir -p results/{bams,peaks,fastqc,motifs} cd data Download data Get the annotation list from the sra run selector IDs.txt Prefetch and convert files to fastq Go into the ~/work/ChIP-seq_/data time parallel -j 10 'prefetch {}' :::: IDs....

Remote desktop Remote desktop can be used to not only work on the remote computer, but also copy clipboard and normal files between the remote computer and your local computer Change settings in the connection Remote Desktop Menu Select “More” in Local Resources Enable Local Discs Locate your local drives File Explorer Sidebar File Explorer Sidebar - detail WSL2 current setup: Name, volumes, environments The WSL2 for bioinformatics is available as “Ubuntu” from the Start menu...

.bashrc # set case insensitivity for the terminal bind "set completion-ignore-case on" # set vim motions on set -o vi .vimrc " set numbering of lines to relative set relativenumber " set formatoptions-=r " set textwidth=80 " if you want to reformat the document, go to start of document and type gqG " set moving up and down centered on the screen nnoremap <C-d> <C-d>zz nnoremap <C-u> <C-u>zz " set the cursor in different modes to be different let &t_EI ="\e[2 q" " block in edit mode let &t_SI ="\e[1 q" " blinking block in insert mode let &t_SR ="\e[3 q" " block in replace mode " set leader to space let mapleader = " " " clear all registers command!...

Extracting relevant columns from csv and tab delimited files. Download as a pdf Exemplary workflow for quick look of papers from pubmed “similar or cited by” Download the citation/similar articles in csv format from pubmed Check the number of lines in the file wc -l file.csv See the names of columns of the file csvcut -n file.csv Create an output for a quick visual check with title and doi, most recent first Option 1: for the output in terminal, comma separated...

Stream editor (sed) edits text files without opening them. Most often, the editing would be a replacement of one character or word by another. This way a delimiter of a csv file can be changed from comma to semicolon, name of a person can be replaced throughout the text. But that is just a beggining; sed has much more to offer: The “word” can be a regular expression making it super flexible The lines where this replacement will be done, can be specified by their line number, range, or content Taken togehter, sed helps to delete, replace, and append characters, words, lines or whole files....

How to manage versions of documents and scripts from the command line. What is a work tree, staging, and commiting?. How can I go back to a previous version of a file? How to branch to test new variant without losing the functional version, how to tag the version. How to push to GitHub from the command mode using ssh authorization. Resource ProGit book link first three chapters are sufficient....

Command line utility ffmpeg, dedicated to different transformations of video, is one of the tools which genuinly feel like magic. ffmpeg download link can do a lot, so it is no surprise that the documentation is overwhelming. Use cases Convert between formats This probably cannot be easier using ffmpeg single video: ffmpeg -i input_video.mp4 output_video.avi multiple videos: for file in *.mp4; do ffmpeg -i "${file}" "${file/.mp4/.avi}" done Video Scale down single video:...

Setting in .bashrc awk defaults to working with whitespace, not with commas, better ot set the comma as an field separator, and otuput field separator and name this modification awkc. Add this to ~/.bashrc # make a csv specific awk alias awkc='awk -F, -v OFS=,' Split a csv file into multiple files based on 3rd column awk -F',' 'NR==1{h=$0;next} {print h > ($3 ".csv"); print >> ($3 ".csv")}' input.csv

🔁 Restore Xubuntu SSD Backup using Macrium Reflect (Windows) This guide explains how to restore a full disk backup of your Xubuntu SSD that was created using Macrium Reflect Free. This is ideal for recovering or migrating your Linux installation (e.g. from backup to a new drive). 🧰 Requirements ✅ A previously created .mrimg backup image (e.g. stored on D: drive) ✅ The drive you want to restore (target SSD) ✅ Macrium Reflect Free installed ✅ Optional: USB drive (to create recovery media if restoring OS disk) 🧪 Step-by-Step Restoration 1....

Converting rgb tif files to cmyk files Looks power point is not able to export tiff into CMYK, only RGB For this process it is important to have the files which define the colour spaces(?) for file in *.TIF; do convert "$file" -profile sRGB_v4_ICC_preference.icc -profile APTEC_PC11_CCNB_2023_v1.icc -density 300 -resize 2550x3300 CMYK_"${file/.TIF/.tiff}"; done Parameters: -density 300 pixels per inch -resize 2550x3300 scale to A4 with a 300 pixels per inch density Resources Profile files:...